Inhibitors of c-jun-n-terminal kinase (jnk)

ABSTRACT

where Ring A, Ring B, X, L1, L2, RA, RC, RD, RE, m, n, and p are as defined herein. Compounds of the present invention are contemplated useful for the prevention and treatment of a variety of human diseases associated with kinase activity, for example, proliferative diseases, neurodegenerative diseases, metabolic disorders, inflammatory diseases, and cardiovascular diseases.

RELATED APPLICATIONS

The present application is a continuation of and claims priority under35 U.S.C. § 120 to U.S. Application, U.S. Ser. No. 14/358,606, filed May15, 2014, which is a national stage filing under 35 U.S.C. § 371 ofinternational PCT application, PCT/US2012/065618, filed Nov. 16, 2012,which claims priority under 35 U.S.C. § 119(e) to U.S. provisionalpatent application, U.S. Ser. No. 61/561,078, filed Nov. 17, 2011, eachof which is incorporated herein by reference.

GOVERNMENT SUPPORT

This invention was made with government support under grant numbersCA148164, HG005693, U54 HG006097, U54 HG006907-01, and NS057135 awardedby the National Institutes of Health. The government has certain rightsin the invention.

BACKGROUND OF THE INVENTION

In mammalian cells, the MAPK (Mitogen-Activated Protein Kinase)signaling system is comprised of, at least, four distinct signalingmodules defined by a core of MAP4K, MAP3K, MAP2K and MAPKs that arenamed after the “terminal” MAPK kinase in each pathway: ERK1/2,JNK1/2/3, p38alpha/beta, and ERKS (Chang et al., 2001; Johnson et al.,2002; Pearson et al., 2001; and Raman et al., 2007). JNKs (c-JunNH₂-terminal kinase) become highly activated after cells are exposed tostress conditions such as cytokines, osmotic stress, hypoxia, and UVlight, and are poorly activated by exposure to growth factors ormitogens (Derijard et al., 1994; and Pulverer et al., 1991). There arethree distinct genes Jnk1, Jnk2, and Jnk3 that are alternatively splicedto yield approximately ten different proteins with the predominantisoforms: JNK1 and JNK2 expressed ubiquitously, and JNK3 expressedprimarily in the nervous system (Derijard et al., 1994; Kallunki et al.,1994; Sluss et al., 1994; and Mohit et al., 1995). JNKs are activated byphosphorylation at the activation T-loop residues Thr183/Tyr185 by theMAP2Ks: MKK4 and MKK7, and are deactivated by MAP kinase phosphatasesincluding MKP1 and MKP5. Signaling through the JNK-pathway is organizedthrough binding to “scaffolding” proteins such as JIP which assemblesignaling complexes containing MAP3K, MAP2K, and MAPKs in addition totranscription factors such as c-Jun, ATF2, and Elk1 which arephosphorylated by JNK. As JNKs comprise a central node in theinflammatory signaling network, it is not surprising thathyperactivation of JNK signaling is a very common finding in a number ofdisease states including cancer, inflammatory, and neurodegenerativediseases. A significant body of genetic and pharmacological evidence hasbeen generated that suggest that inhibitors of JNK signaling may providea promising therapeutic strategy. JNK3 knockout mice exhibitamelioration of neurodegeneration in animal models of Parkinson's andAlzheimer's disease (Kyriakis et al., 2001; Zhang et al., 2005; andHunot et al., 2004). JNK1 phosphorylates IRS-1, a key molecule in theinsulin-sensing pathway which down-regulates insulin signaling, and JNK1knockout mice are resistant to diet-induced obesity (Aguirre et al.,2000 and 2002; Hirosumi et al., 2002; and Sabio et al., 2010) . JNK2,often in concert with JNK1, has been implicated in the pathology ofautoimmune disorders such as rheumatoid arthritis (Han et al., 2002) andasthma (Wong, W.S., 2005; Pelaia et al., 2005; Blease et al., 2003;Chialda et al., 2005); A recent study suggests that JNK2 may play a rolein vascular disease and atherosclerosis as well (Osto et al., 2008).Yet, to date, no direct JNK inhibitors have been approved for use inhumans.

Numerous small molecules from a variety of scaffolds such as indazoles,aminopyrazoles, aminopyridines, pyridine carboxamides,benzothien-2-ylamides and benzothiazol-2-yl acetonitriles, quinolinederivatives, and aminopyrimidines have been reported to act as selectiveATP-competitive JNK inhibitors (LoGrasso and Kamenecka, 2008). However,despite this apparent plethora of reported JNK inhibitors, many exhibitpoor kinase selectivity and/or do not inhibit the phosphorylation ofwell characterized substrates of JNK in cells. For example, one of theearliest and still most widely utilized inhibitors is theanthrapyrazolone, SP-600125 (Bennett et al., 2001) (FIG. 1) whichexhibits exceptionally low specificity for JNK (Bain et al., 2007) andshould only be used in combination with other approaches such as genedeletions or siRNA mediated depletion to rule-out a JNK role in aparticular process (Inesta-Vaquera et al., 2010). Other reported JNKinhibitors such as AS601245 (Gaillard et al., 2005) only inhibit c-Junphosphorylation at high concentrations which is likely due to acombination of limited cell penetration, ATP concentration, anddifferences between biochemical and cellular sensitivities to JNKinhibitors.

SUMMARY OF THE INVENTION

The mitogen activated c-Jun-N-terminal kinases (JNKs, such as JNK1,JNK2, and JNK3) are key enzymes in signaling modules that transduce andintegrate extracellular stimuli into coordinated cellular response.Irreversible JNK inhibitors, such as JNK-IN-7, were discovered to form acovalent bond with a cysteine residue conserved in JNKs. Someirreversible JNK inhibitors, such as JNK-IN-8, are selective JNKinhibitors that inhibit c-Jun phosphorylation, a direct JNK substrate,in cells in a manner that was dependent on covalent modification of theconserved cysteine residue. Extensive biochemical, cellular, andpathway-based profiling were used to establish the JNK selectivity ofthese compounds and suggested their applicability as versatilepharmacological probes of JNK-mediated biological phenomena.

The present invention provides compounds of Formula (I), andpharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,prodrugs, and compositions thereof. The present invention furtherprovides methods of using the inventive compounds, and pharmaceuticallyacceptable salts, solvates, hydrates, polymorphs, co-crystals,tautomers, stereoisomers, isotopically labeled derivatives, prodrugs,and compositions thereof, to study the inhibition of JNK and astherapeutics for the prevention and treatment of diseases associatedwith JNK activity. In certain embodiments, the inventive compounds areused for the prevention and treatment of proliferative diseases (e.g.,cancer and benign neoplasms), neurodegenerative diseases, metabolicdisorders, inflammatory diseases, and cardiovascular diseases.

In one aspect, the present invention provides compounds of Formula (I):

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,and prodrugs thereof, wherein Ring A, Ring B, X, L¹, L², R^(A), R^(C),R^(D), R^(E), m, n, and p are as defined herein.

Exemplary compounds of Formulae (I) include, but are not limited to:

In another aspect, the present invention provides pharmaceuticalcompositions comprising a compound of Formulae (I) and pharmaceuticallyacceptable salts, solvates, hydrates, polymorphs, co-crystals,tautomers, stereoisomers, isotopically labeled derivatives, and prodrugsthereof, and optionally a pharmaceutically acceptable excipient.

In still another aspect, the invention provides methods and compositionsfor the treatment of diseases of a subject. The diseases being treatedby the inventive methods include JNK-associated diseases. Inhibition ofother therapeutic targets and their associated diseases, such as CDK7and CDK7-associated diseases, are contemplated herein. Exemplarydiseases include, but are not limited to, neurodegenerative diseases,metabolic disorders, inflammatory diseases, cardiovascular diseases, andproliferative diseases (e.g., cancer and benign neoplasms). The methodsof the invention include administering to a subject in need of treatmentof a disease a therapeutically effective amount of a compound of thepresent invention. The compound of the present invention may be, e.g.,JNK-IN-5, JNK-IN-6, JNK-IN-7, JNK-IN-8, JNK-IN-9, JNK-IN-10, JNK-IN-11,and JNK-IN-12, or a pharmaceutically acceptable salt, solvate, hydrate,polymorph, co-crystal, tautomer, stereoisomer, isotopically labeledderivative, or prodrug thereof.

The details of one or more embodiments of the invention are set forthherein. Other features, objects, and advantages of the invention will beapparent from the Detailed Description, the Figures, the Examples, andthe Claims.

Definitions

Definitions of specific functional groups and chemical terms aredescribed in more detail below. The chemical elements are identified inaccordance with the Periodic Table of the Elements, CAS version,Handbook of Chemistry and Physics, 75^(th) Ed., inside cover, andspecific functional groups are generally defined as described therein.Additionally, general principles of organic chemistry, as well asspecific functional moieties and reactivity, are described in ThomasSorrell, Organic Chemistry, University Science Books, Sausalito, 1999;Smith and March, March's Advanced Organic Chemistry, 5^(th) Edition,John Wiley & Sons, Inc., New York, 2001; Larock, Comprehensive OrganicTransformations, VCH Publishers, Inc., New York, 1989; and Carruthers,Some Modern Methods of Organic Synthesis, 3^(rd) Edition, CambridgeUniversity Press, Cambridge, 1987.

Compounds described herein can comprise one or more asymmetric centers,and thus can exist in various isomeric forms, e.g., enantiomers and/ordiastereomers. For example, the compounds described herein can be in theform of an individual enantiomer, diastereomer or geometric isomer, orcan be in the form of a mixture of stereoisomers, including racemicmixtures and mixtures enriched in one or more stereoisomer. Isomers canbe isolated from mixtures by methods known to those skilled in the art,including chiral high pressure liquid chromatography (HPLC) and theformation and crystallization of chiral salts; or preferred isomers canbe prepared by asymmetric syntheses. See, for example, Jacques et al.,Enantiomers, Racemates and Resolutions (Wiley Interscience, New York,1981); Wilen et al., Tetrahedron 33:2725 (1977); Eliel, Stereochemistryof Carbon Compounds (McGrawHill, N.Y., 1962); and Wilen, Tables ofResolving Agents and Optical Resolutions p. 268 (E. L. Eliel, Ed., Univ.of Notre Dame Press, Notre Dame, Ind. 1972). The invention additionallyencompasses compounds described herein as individual isomerssubstantially free of other isomers, and alternatively, as mixtures ofvarious isomers.

When a range of values is listed, it is intended to encompass each valueand sub-range within the range. For example “C₁₋₆” is intended toencompass, C₁, C₂, C₃, C₄, C₅, C₆, C₁₋₆, C_(1-5, C) ₁₋₄, C₁₋₃, C₁₋₂,C₂₋₆, C₂₋₅, C₂₋₄, C₂₋₃, C₃₋₆, C₃₋₅, C₃₋₄, C₄₋₆, C₄₋₅, and C₅₋₆.

As used herein, a “hydrocarbon chain” refers to a substituted orunsubstituted divalent alkyl, alkenyl, or alkynyl group. A hydrocarbonchain includes at least one chain, each node (“carbon unit”) of whichincluding at least one carbon atom, between the two radicals of thehydrocarbon chain. For example, hydrocarbon chain—C^(A)H(C^(B)H₂C^(C)H₃) includes only one carbon unit C^(A). The term“C_(x) hydrocarbon chain,” wherein x is a positive integer, refers to ahydrocarbon chain that includes x number of carbon unit(s) between thetwo radicals of the hydrocarbon chain. If there is more than onepossible value of x, the smallest possible value of x is used for thedefinition of the hydrocarbon chain. For example, —CH(C₂H₅) is a C₁hydrocarbon chain, and

is a C₃ hydrocarbon chain. When a range of values is used, e.g., a C₁₋₆hydrocarbon chain, the meaning of the range is as described herein. Ahydrocarbon chain may be saturated (e.g., —(CH₂)₄—). A hydrocarbon chainmay also be unsaturated and include one or more C═C and/or C≡C bondsanywhere in the hydrocarbon chain. For instance, —CH═CH(CH₂)₂—,—CH₂C≡C—CH₂, and —C≡C—CH═CH— are all examples of a unsubstituted andunsaturated hydrocarbon chain. In certain embodiments, the hydrocarbonchain is unsubstituted (e.g., —(CH₂)₄—). In certain embodiments, thehydrocarbon chain is substituted (e.g., —CH(C₂H₅)— and —CF₂—). Any twosubstituents on the hydrocarbon chain may be joined to form anoptionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, or optionally substituted heteroaryl ring.For instance,

are all examples of a hydrocarbon chain. In contrast, in certainembodiments

are not within the scope of the hydrocarbon chains described herein.

“Alkyl” refers to a radical of a straightchain or branched saturatedhydrocarbon group having from 1 to 20 carbon atoms (“C₁₋₂₀ alkyl”). Insome embodiments, an alkyl group has 1 to 10 carbon atoms (“C₁₋₁₀alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms(“C₁₋₉ alkyl”). In some embodiments, an alkyl group has 1 to 8 carbonatoms (“C₁₋₈ alkyl”). In some embodiments, an alkyl group has 1 to 7carbon atoms (“C₁₋₇ alkyl”). In some embodiments, an alkyl group has 1to 6 carbon atoms (“C₁₋₆ alkyl”). In some embodiments, an alkyl grouphas 1 to 5 carbon atoms (“C₁₋₅ alkyl”). In some embodiments, an alkylgroup has 1 to 4 carbon atoms (“C₁₋₄ alkyl”). In some embodiments, analkyl group has 1 to 3 carbon atoms (“C₁₋₃ alkyl”). In some embodiments,an alkyl group has 1 to 2 carbon atoms (“C₁₋₂ alkyl”). In someembodiments, an alkyl group has 1 carbon atom (“C₁ alkyl”). In someembodiments, an alkyl group has 2 to 6 carbon atoms (“C₂₋₆ alkyl”).Examples of C₁₋₆ alkyl groups include methyl (C₁), ethyl (C₂), npropyl(C₃), isopropyl (C₃), nbutyl (C₄), tertbutyl (C₄), secbutyl (C₄), isobutyl (C₄), n-pentyl (C₅), 3-pentanyl (C₅), amyl (C₅), neopentyl (C₅),3-methyl-2-butanyl (C₅), tertiary amyl (C₅), and n-hexyl (C₆).Additional examples of alkyl groups include n-heptyl (C₇), n-octyl (C₈)and the like. Unless otherwise specified, each instance of an alkylgroup is independently optionally substituted, i.e., unsubstituted (an“unsubstituted alkyl”) or substituted (a “substituted alkyl”) with oneor more substituents. In certain embodiments, the alkyl group isunsubstituted C₁₋₁₀ alkyl (e.g., —CH₃). In certain embodiments, thealkyl group is substituted C₁₋₁₀ alkyl.

“Alkenyl” refers to a radical of a straightchain or branched hydrocarbongroup having from 2 to 20 carbon atoms, one or more carboncarbon doublebonds, and no triple bonds (“C₂₋₂₀ alkenyl”). In some embodiments, analkenyl group has 2 to 10 carbon atoms (“C₂ ₁₀ alkenyl”). In someembodiments, an alkenyl group has 2 to 9 carbon atoms (“C₂₋₉ alkenyl”).In some embodiments, an alkenyl group has 2 to 8 carbon atoms (“C₂₋₈alkenyl”). In some embodiments, an alkenyl group has 2 to 7 carbon atoms(“C₂₋₇ alkenyl”). In some embodiments, an alkenyl group has 2 to 6carbon atoms (“C₂₋₆ alkenyl”). In some embodiments, an alkenyl group has2 to 5 carbon atoms (“C₂₋₅ alkenyl”). In some embodiments, an alkenylgroup has 2 to 4 carbon atoms (“C₂₋₄ alkenyl”). In some embodiments, analkenyl group has 2 to 3 carbon atoms (“C₂₋₃ alkenyl”). In someembodiments, an alkenyl group has 2 carbon atoms (“C₂ alkenyl”). The oneor more carboncarbon double bonds can be internal (such as in 2-butenyl)or terminal (such as in 1-butenyl). Examples of C₂₋₄ alkenyl groupsinclude ethenyl (C₂), 1-propenyl (C₃), 2-propenyl (C₃), 1-butenyl (C₄),2-butenyl (C₄), butadienyl (C₄), and the like. Examples of C₂₋₆ alkenylgroups include the aforementioned C₂₋₄ alkenyl groups as well aspentenyl (C₅), pentadienyl (C₅), hexenyl (C₆), and the like. Additionalexamples of alkenyl include heptenyl (C₇), octenyl (C₈), octatrienyl(C₈), and the like. Unless otherwise specified, each instance of analkenyl group is independently optionally substituted, i.e.,unsubstituted (an “unsubstituted alkenyl”) or substituted (a“substituted alkenyl”) with one or more substituents. In certainembodiments, the alkenyl group is unsubstituted C₂₋₁₀ alkenyl. Incertain embodiments, the alkenyl group is substituted C₂₋₁₀ alkenyl.

“Alkynyl” refers to a radical of a straightchain or branched hydrocarbongroup having from 2 to 20 carbon atoms, one or more carboncarbon triplebonds, and optionally one or more double bonds (“C₂ ₂₀ alkynyl”). Insome embodiments, an alkynyl group has 2 to 10 carbon atoms (“C₂₋₁₀alkynyl”). In some embodiments, an alkynyl group has 2 to 9 carbon atoms(“C₂₋₉ alkynyl”). In some embodiments, an alkynyl group has 2 to 8carbon atoms (“C₂₋₈ alkynyl”). In some embodiments, an alkynyl group has2 to 7 carbon atoms (“C₂₋₇ alkynyl”). In some embodiments, an alkynylgroup has 2 to 6 carbon atoms (“C₂₋₆ alkynyl”). In some embodiments, analkynyl group has 2 to 5 carbon atoms (“C₂₋₅ alkynyl”). In someembodiments, an alkynyl group has 2 to 4 carbon atoms (“C₂₋₄ alkynyl”).In some embodiments, an alkynyl group has 2 to 3 carbon atoms (“C₂₋₃alkynyl”). In some embodiments, an alkynyl group has 2 carbon atoms (“C₂alkynyl”). The one or more carboncarbon triple bonds can be internal(such as in 2-butynyl) or terminal (such as in 1-butynyl). Examples ofC₂₋₄ alkynyl groups include, without limitation, ethynyl (C₂),1-propynyl (C₃), 2-propynyl (C₃), 1-butynyl (C₄), 2-butynyl (C₄), andthe like. Examples of C₂₋₆ alkenyl groups include the aforementionedC₂₋₄ alkynyl groups as well as pentynyl (C₅), hexynyl (C₆), and thelike. Additional examples of alkynyl include heptynyl (C₇), octynyl(C₈), and the like. Unless otherwise specified, each instance of analkynyl group is independently optionally substituted, i.e.,unsubstituted (an “unsubstituted alkynyl”) or substituted (a“substituted alkynyl”) with one or more substituents. In certainembodiments, the alkynyl group is unsubstituted C₂₋₁₀ alkynyl. Incertain embodiments, the alkynyl group is substituted C₂₋₁₀ alkynyl.

“Carbocyclyl” or “carbocyclic” refers to a radical of a nonaromaticcyclic hydrocarbon group having from 3 to 10 ring carbon atoms (“C₃₋₁₀carbocyclyl”) and zero heteroatoms in the nonaromatic ring system. Insome embodiments, a carbocyclyl group has 3 to 8 ring carbon atoms(“C₃₋₈ carbocyclyl”). In some embodiments, a carbocyclyl group has 3 to6 ring carbon atoms (“C₃₋₆ carbocyclyl”). In some embodiments, acarbocyclyl group has 3 to 6 ring carbon atoms (“C₃₋₆ carbocyclyl”). Insome embodiments, a carbocyclyl group has 5 to 10 ring carbon atoms(“C₅₋₁₀ carbocyclyl”). Exemplary C₃₋₆ carbocyclyl groups include,without limitation, cyclopropyl (C₃), cyclopropenyl (C₃), cyclobutyl(C₄), cyclobutenyl (C₄), cyclopentyl (C₅), cyclopentenyl (C₅),cyclohexyl (C₆), cyclohexenyl (C₆), cyclohexadienyl (C₆), and the like.Exemplary C₃₋₈ carbocyclyl groups include, without limitation, theaforementioned C₃₋₆ carbocyclyl groups as well as cycloheptyl (C₇),cycloheptenyl (C₇), cycloheptadienyl (C₇), cycloheptatrienyl (C₇),cyclooctyl (C₈), cyclooctenyl (C₈), bicyclo[2.2.1]heptanyl (C₇),bicyclo[2.2.2]octanyl (C₈), and the like. Exemplary C₃ ₁₀ carbocyclylgroups include, without limitation, the aforementioned C₃₋₈ carbocyclylgroups as well as cyclononyl (C₉), cyclononenyl (C₉), cyclodecyl (C₁₀),cyclodecenyl (C₁₀), octahydro-1H-indenyl (C₉), decahydronaphthalenyl(C₁₀), spiro[4.5]decanyl (C₁₀), and the like. As the foregoing examplesillustrate, in certain embodiments, the carbocyclyl group is eithermonocyclic (“monocyclic carbocyclyl”) or contain a fused, bridged orspiro ring system such as a bicyclic system (“bicyclic carbocyclyl”) andcan be saturated or can be partially unsaturated. “Carbocyclyl” alsoincludes ring systems wherein the carbocyclic ring, as defined above, isfused with one or more aryl or heteroaryl groups wherein the point ofattachment is on the carbocyclic ring, and in such instances, the numberof carbons continue to designate the number of carbons in thecarbocyclic ring system. Unless otherwise specified, each instance of acarbocyclyl group is independently optionally substituted, i.e.,unsubstituted (an “unsubstituted carbocyclyl”) or substituted (a“substituted carbocyclyl”) with one or more substituents. In certainembodiments, the carbocyclyl group is unsubstituted C₃₋₁₀ carbocyclyl.In certain embodiments, the carbocyclyl group is a substituted C₃₋₁₀carbocyclyl.

In some embodiments, “carbocyclyl” is a monocyclic, saturatedcarbocyclyl group having from 3 to 10 ring carbon atoms (“C₃₋₁₀cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 8 ringcarbon atoms (“C₃₋₈ cycloalkyl”). In some embodiments, a cycloalkylgroup has 3 to 6 ring carbon atoms (“C₃₋₆ cycloalkyl”). In someembodiments, a cycloalkyl group has 5 to 6 ring carbon atoms (“C₅₋₆cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 10 ringcarbon atoms (“C₅₋₁₀ cycloalkyl”). Examples of C₅₋₆ cycloalkyl groupsinclude cyclopentyl (C₅) and cyclohexyl (C₅). Examples of C₃₋₆cycloalkyl groups include the aforementioned C₅₋₆ cycloalkyl groups aswell as cyclopropyl (C₃) and cyclobutyl (C₄). Examples of C₃₋₈cycloalkyl groups include the aforementioned C₃₋₆ cycloalkyl groups aswell as cycloheptyl (C₇) and cyclooctyl (C₈). Unless otherwisespecified, each instance of a cycloalkyl group is independentlyunsubstituted (an “unsubstituted cycloalkyl”) or substituted (a“substituted cycloalkyl”) with one or more substituents. In certainembodiments, the cycloalkyl group is unsubstituted C₃₋₁₀ cycloalkyl. Incertain embodiments, the cycloalkyl group is substituted C₃₋₁₀cycloalkyl.

“Heterocyclyl” or “heterocyclic” refers to a radical of a 3to 10memberednon-aromatic ring system having ring carbon atoms and 1 to 4 ringheteroatoms, wherein each heteroatom is independently selected fromnitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“3-10 memberedheterocyclyl”). In heterocyclyl groups that contain one or more nitrogenatoms, the point of attachment can be a carbon or nitrogen atom, asvalency permits. A heterocyclyl group can either be monocyclic(“monocyclic heterocyclyl”) or a fused, bridged or spiro ring systemsuch as a bicyclic system (“bicyclic heterocyclyl”), and can besaturated or can be partially unsaturated. Heterocyclyl bicyclic ringsystems can include one or more heteroatoms in one or both rings.“Heterocyclyl” also includes ring systems wherein the heterocyclic ring,as defined above, is fused with one or more carbocyclyl groups whereinthe point of attachment is either on the carbocyclyl or heterocyclicring, or ring systems wherein the heterocyclic ring, as defined above,is fused with one or more aryl or heteroaryl groups, wherein the pointof attachment is on the heterocyclic ring, and in such instances, thenumber of ring members continue to designate the number of ring membersin the heterocyclic ring system. Unless otherwise specified, eachinstance of heterocyclyl is independently optionally substituted, i.e.,unsubstituted (an “unsubstituted heterocyclyl”) or substituted (a“substituted heterocyclyl”) with one or more substituents. In certainembodiments, the heterocyclyl group is unsubstituted 3-10 memberedheterocyclyl. In certain embodiments, the heterocyclyl group issubstituted 3-10 membered heterocyclyl.

In some embodiments, a heterocyclyl group is a 5-10 membered nonaromaticring system having ring carbon atoms and 1-4 ring heteroatoms, whereineach heteroatom is independently selected from nitrogen, oxygen, sulfur,boron, phosphorus, and silicon (“5-10 membered heterocyclyl”). In someembodiments, a heterocyclyl group is a 5-8 membered non-aromatic ringsystem having ring carbon atoms and 1-4 ring heteroatoms, wherein eachheteroatom is independently selected from nitrogen, oxygen, and sulfur(“5-8 membered heterocyclyl”). In some embodiments, a heterocyclyl groupis a 5-6 membered nonaromatic ring system having ring carbon atoms and1-4 ring heteroatoms, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-6 membered heterocyclyl”). In someembodiments, the 5-6 membered heterocyclyl has 1-3 ring heteroatomsselected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6membered heterocyclyl has 1-2 ring heteroatoms selected from nitrogen,oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclylhas one ring heteroatom selected from nitrogen, oxygen, and sulfur.

Exemplary 3membered heterocyclyl groups containing one heteroatominclude, without limitation, azirdinyl, oxiranyl, thiorenyl. Exemplary4membered heterocyclyl groups containing one heteroatom include, withoutlimitation, azetidinyl, oxetanyl and thietanyl. Exemplary 5memberedheterocyclyl groups containing one heteroatom include, withoutlimitation, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl,dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl and pyrrolyl-2,5-dione.Exemplary 5-membered heterocyclyl groups containing two heteroatomsinclude, without limitation, dioxolanyl, oxasulfuranyl, disulfuranyl,and oxazolidin-2-one. Exemplary 5-membered heterocyclyl groupscontaining three heteroatoms include, without limitation, triazolinyl,oxadiazolinyl, and thiadiazolinyl. Exemplary 6-membered heterocyclylgroups containing one heteroatom include, without limitation,piperidinyl, tetrahydropyranyl, dihydropyridinyl, and thianyl. Exemplary6-membered heterocyclyl groups containing two heteroatoms include,without limitation, piperazinyl, morpholinyl, dithianyl, dioxanyl.Exemplary 6-membered heterocyclyl groups containing two heteroatomsinclude, without limitation, triazinanyl. Exemplary 7-memberedheterocyclyl groups containing one heteroatom include, withoutlimitation, azepanyl, oxepanyl and thiepanyl. Exemplary 8-memberedheterocyclyl groups containing one heteroatom include, withoutlimitation, azocanyl, oxecanyl and thiocanyl. Exemplary 5-memberedheterocyclyl groups fused to a C₆ aryl ring (also referred to herein asa 5,6-bicyclic heterocyclic ring) include, without limitation,indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl,benzoxazolinonyl, and the like. Exemplary 6-membered heterocyclyl groupsfused to an aryl ring (also referred to herein as a 6,6-bicyclicheterocyclic ring) include, without limitation, tetrahydroquinolinyl,tetrahydroisoquinolinyl, and the like.

“Aryl” refers to a radical of a monocyclic or polycyclic (e.g., bicyclicor tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 πelectrons shared in a cyclic array) having 6-14 ring carbon atoms andzero heteroatoms provided in the aromatic ring system (“C₆₋₁₄ aryl”). Insome embodiments, an aryl group has six ring carbon atoms (“C₆ aryl”;e.g., phenyl). In some embodiments, an aryl group has ten ring carbonatoms (“C₁₀ aryl”; e.g., naphthyl such as 1-naphthyl and 2-naphthyl). Insome embodiments, an aryl group has fourteen ring carbon atoms (“C₁₄aryl”; e.g., anthracyl). “Aryl” also includes ring systems wherein thearyl ring, as defined above, is fused with one or more carbocyclyl orheterocyclyl groups wherein the radical or point of attachment is on thearyl ring, and in such instances, the number of carbon atoms continue todesignate the number of carbon atoms in the aryl ring system. Unlessotherwise specified, each instance of an aryl group is independentlyoptionally substituted, i.e., unsubstituted (an “unsubstituted aryl”) orsubstituted (a “substituted aryl”) with one or more substituents. Incertain embodiments, the aryl group is unsubstituted C₆₋₁₄ aryl. Incertain embodiments, the aryl group is substituted C₆₋₁₄ aryl.

“Aralkyl” is a subset of alkyl and aryl, as defined herein, and refersto an optionally substituted alkyl group substituted by an optionallysubstituted aryl group.

“Heteroaryl” refers to a radical of a 5-10 membered monocyclic orbicyclic 4n+2 aromatic ring system (e.g., having 6 or 10 π electronsshared in a cyclic array) having ring carbon atoms and 1-4 ringheteroatoms provided in the aromatic ring system, wherein eachheteroatom is independently selected from nitrogen, oxygen and sulfur(“5-10 membered heteroaryl”). In heteroaryl groups that contain one ormore nitrogen atoms, the point of attachment can be a carbon or nitrogenatom, as valency permits. Heteroaryl bicyclic ring systems can includeone or more heteroatoms in one or both rings. “Heteroaryl” includes ringsystems wherein the heteroaryl ring, as defined above, is fused with oneor more carbocyclyl or heterocyclyl groups wherein the point ofattachment is on the heteroaryl ring, and in such instances, the numberof ring members continue to designate the number of ring members in theheteroaryl ring system. “Heteroaryl” also includes ring systems whereinthe heteroaryl ring, as defined above, is fused with one or more arylgroups wherein the point of attachment is either on the aryl orheteroaryl ring, and in such instances, the number of ring membersdesignates the number of ring members in the fused (aryl/heteroaryl)ring system. Bicyclic heteroaryl groups wherein one ring does notcontain a heteroatom (e.g., indolyl, quinolinyl, carbazolyl, and thelike) the point of attachment can be on either ring, i.e., either thering bearing a heteroatom (e.g., 2-indolyl) or the ring that does notcontain a heteroatom (e.g., 5-indolyl).

In some embodiments, a heteroaryl group is a 5-10 membered aromatic ringsystem having ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-10 membered heteroaryl”). In someembodiments, a heteroaryl group is a 5-8 membered aromatic ring systemhaving ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-8 membered heteroaryl”). In someembodiments, a heteroaryl group is a 5-6 membered aromatic ring systemhaving ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-6 membered heteroaryl”). In someembodiments, the 5-6 membered heteroaryl has 1-3 ring heteroatomsselected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen,oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has1 ring heteroatom selected from nitrogen, oxygen, and sulfur. Unlessotherwise specified, each instance of a heteroaryl group isindependently optionally substituted, i.e., unsubstituted (an“unsubstituted heteroaryl”) or substituted (a “substituted heteroaryl”)with one or more substituents. In certain embodiments, the heteroarylgroup is unsubstituted 5-14 membered heteroaryl. In certain embodiments,the heteroaryl group is substituted 5-14 membered heteroaryl.

Exemplary 5-membered heteroaryl groups containing one heteroatominclude, without limitation, pyrrolyl, furanyl and thiophenyl. Exemplary5-membered heteroaryl groups containing two heteroatoms include, withoutlimitation, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, andisothiazolyl. Exemplary 5-membered heteroaryl groups containing threeheteroatoms include, without limitation, triazolyl, oxadiazolyl, andthiadiazolyl. Exemplary 5-membered heteroaryl groups containing fourheteroatoms include, without limitation, tetrazolyl. Exemplary6-membered heteroaryl groups containing one heteroatom include, withoutlimitation, pyridinyl. Exemplary 6-membered heteroaryl groups containingtwo heteroatoms include, without limitation, pyridazinyl, pyrimidinyl,and pyrazinyl. Exemplary 6-membered heteroaryl groups containing threeor four heteroatoms include, without limitation, triazinyl andtetrazinyl, respectively. Exemplary 7-membered heteroaryl groupscontaining one heteroatom include, without limitation, azepinyl,oxepinyl, and thiepinyl. Exemplary 5,6-bicyclic heteroaryl groupsinclude, without limitation, indolyl, isoindolyl, indazolyl,benzotriazolyl, benzothiophenyl, isobenzothiophenyl, benzofuranyl,benzoisofuranyl, benzimidazolyl, benzoxazolyl, benzisoxazolyl,benzoxadiazolyl, benzthiazolyl, benzisothiazolyl, benzthiadiazolyl,indolizinyl, and purinyl. Exemplary 6,6-bicyclic heteroaryl groupsinclude, without limitation, naphthyridinyl, pteridinyl, quinolinyl,isoquinolinyl, cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl.

“Heteroaralkyl” is a subset of alkyl and heteroaryl, as defined herein,and refers to an optionally substituted alkyl group substituted by anoptionally substituted heteroaryl group.

“Partially unsaturated” refers to a group that includes at least onedouble or triple bond. A “partially unsaturated” ring system is furtherintended to encompass rings having multiple sites of unsaturation, butis not intended to include aromatic groups (e.g., aryl or heteroarylgroups) as herein defined. Likewise, “saturated” refers to a group thatdoes not contain a double or triple bond, i.e., contains all singlebonds.

Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroarylgroups, as defined herein, which are divalent bridging groups arefurther referred to using the suffix -ene, e.g., alkylene, alkenylene,alkynylene, carbocyclylene, heterocyclylene, arylene, and heteroarylene.

Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroarylgroups, as defined herein, are optionally substituted (e.g.,“substituted” or “unsubstituted” alkyl, “substituted” or “unsubstituted”alkenyl, “substituted” or “unsubstituted” alkynyl, “substituted” or“unsubstituted” carbocyclyl, “substituted” or “unsubstituted”heterocyclyl, “substituted” or “unsubstituted” aryl or “substituted” or“unsubstituted” heteroaryl group). In general, the term “substituted”,whether preceded by the term “optionally” or not, means that at leastone hydrogen present on a group (e.g., a carbon or nitrogen atom) isreplaced with a permissible substituent, e.g., a substituent which uponsubstitution results in a stable compound, e.g., a compound which doesnot spontaneously undergo transformation such as by rearrangement,cyclization, elimination, or other reaction. Unless otherwise indicated,a “substituted” group has a substituent at one or more substitutablepositions of the group, and when more than one position in any givenstructure is substituted, the substituent is either the same ordifferent at each position. The term “substituted” is contemplated toinclude substitution with all permissible substituents of organiccompounds, any of the substituents described herein that results in theformation of a stable compound. The present invention contemplates anyand all such combinations in order to arrive at a stable compound. Forpurposes of this invention, heteroatoms such as nitrogen may havehydrogen substituents and/or any suitable substituent as describedherein which satisfy the valencies of the heteroatoms and results in theformation of a stable moiety.

Exemplary carbon atom substituents include, but are not limited to,halogen, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, —OH, —OR^(aa), —ON(R^(bb))₂,—N(R^(bb))₂, —N(R^(bb))₃ ⁺X⁻, —N(OR^(cc))R^(bb), —SH, —SR^(aa),—SSR^(cc), —C(═O)R^(aa), —CO₂H, —CHO, —C(OR^(cc))₂, —CO₂R^(aa),—OC(═O)R^(aa), —OCO₂R^(aa), —C(═O)N(R^(bb))₂, —OC(═O)N(R^(bb))₂,—NR^(bb)C(═O)R^(aa), —NR^(bb)CO₂R^(aa), —NR^(bb)C(═O)N(R^(bb))₂,—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —OC(═NR^(bb))R^(aa),—OC(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂, —OC(═NR^(bb))N(R^(bb))₂,—NR^(bb)C(═NR^(bb))N(R^(bb))₂, —C(═O)NR^(bb)SO₂R^(aa),—NR^(bb)SO₂R^(aa), —SO₂N(R^(bb))₂, —SO₂R^(aa), —SO₂OR^(aa), —OSO₂R^(aa),—S(═O)R^(aa), —OS(═O)R^(aa), —Si(R^(aa))₃,—OSi(R^(aa))₃—C(═S)N(R^(bb))₂, —C(═O)SR^(aa), —C(═S)SR^(aa),—SC(═S)SR^(aa), —SC(═O)SR^(aa), —OC(═O)SR^(aa), —SC(═O)OR^(aa),—SC(═O)R^(aa), —P(═O)₂R^(aa), —OP(═O)₂R^(aa), —P(═O)(R^(aa))₂,—OP(═O)(R^(aa))₂, —OP(═O)(OR^(cc))₂, —P(═O)₂N(R^(bb))₂,—OP(═O)₂N(R^(bb))₂, —P(═O)(NR^(bb))₂, —OP(═O)(NR^(bb))₂,—NR^(bb)P(═O)(OR^(cc))₂, —NR^(bb)P(═O)(NR^(bb))₂, —P(R^(cc))₂,—P(R^(cc))₃, —OP(R^(cc))₂, —OP(R^(cc))₃, —B(R^(aa))₂, —B(OR^(cc))₂,—BR^(aa)(OR^(cc)), C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and5-14 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, and heteroaryl is independentlysubstituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

or two geminal hydrogens on a carbon atom are replaced with the group═O, ═S, ═NN(R^(bb))₂, ═NNR^(bb)C(═O)R^(aa), ═NNR^(bb)C(═O)OR^(aa),═NNR^(bb)S(═O)₂R^(aa), ═NR^(bb), or ═NOR^(cc);

each instance of R^(aa) is, independently, selected from C₁₋₁₀ alkyl,C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl,3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, ortwo R^(aa) groups are joined to form a 3-14 membered heterocyclyl or5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, and heteroaryl is independentlysubstituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(bb) is, independently, selected from hydrogen, —OH,—OR^(aa), —N(R^(cc))₂, —CN, —C(═O)R^(aa), —C(═O)N(R^(cc))₂, —CO₂R^(aa),—SO₂R^(aa), —C(═NR^(cc))OR^(aa), —C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂,—SO₂R^(cc), —SO₂OR^(cc), —SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc),—C(═S)SR^(cc), —P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)₂N(R^(cc))₂,—P(═O)(NR^(cc))₂, C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and5-14 membered heteroaryl, or two R^(bb) groups are joined to form a 3-14membered heterocyclyl or 5-14 membered heteroaryl ring, wherein eachalkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroarylis independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(cc) is, independently, selected from hydrogen, C₁₋₁₀alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 memberedheteroaryl, or two R^(cc) groups are joined to form a 3-14 memberedheterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl,alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl isindependently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(dd) is, independently, selected from halogen, —CN,—NO₂, —N₃, —SO₂H, —SO₃H, —OH, —OR^(cc), —ON(R^(ff))₂, —N(R^(ff))₂,—N(R^(ff))₃ ⁺X⁻, —N(OR^(cc))R^(ff), —SH, —SR^(cc), —SSR^(ee),—C(═O)R^(cc), —CO₂H, —CO₂R^(cc), —OC(═O)R^(cc), —OCO₂R^(cc),—C(═O)N(R^(ff))₂, —OC(═O)N(R^(ff))₂, —NR^(ff)C(═O)R^(cc),—NR^(ff)CO₂R^(cc), —NR^(ff)C(═O)N(R^(ff))₂, —C(═NR^(ff))OR^(cc),—OC(═NR^(ff))R^(cc), —OC(═NR^(ff))OR^(cc), —C(═NR^(ff))N(R^(ff))₂,—OC(═NR^(ff))N(R^(ff))₂, —NR^(ff)C(═NR^(ff))N(R^(ff))₂,—NR^(ff)SO₂R^(cc), —SO₂N(R^(ff))₂, —SO₂R^(cc), —SO₂OR^(cc), —OSO₂R^(cc),—S(═O)R^(cc),—Si(R^(cc))₃, —OSi(R^(cc))₃, —C(═S)N(R^(ff))₂,—C(═O)SR^(ee), —C(═S)SR^(ee), —SC(═S)SR^(ee), —P(═O)₂R^(ee),—P(═O)(R^(ee))₂, —OP(═O)(R^(ee))₂, —OP(═O)(OR^(ee))₂, C₁₋₆ alkyl, C₁₋₆perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl, 3-10membered heterocyclyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, whereineach alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, andheteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(gg)groups, or two geminal R^(dd) substituents can be joined to form ═O or═S;

each instance of R^(ee) is, independently, selected from C₁₋₆ alkyl,C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl, C₆₋₁₀aryl, 3-10 membered heterocyclyl, and 3-10 membered heteroaryl, whereineach alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, andheteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(gg)groups;

each instance of R^(ff) is, independently, selected from hydrogen, C₁₋₆alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl,3-10 membered heterocyclyl, C₆₋₁₀ aryl and 5-10 membered heteroaryl, ortwo e groups are joined to form a 3-14 membered heterocyclyl or 5-14membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, and heteroaryl is independentlysubstituted with 0,1,2,3,4, or 5 R^(gg) groups; and

each instance of R^(gg) is, independently, halogen, —CN, —NO₂, —N₃,—SO₂H, —SO₃H, —OH, —OC₁₋₆ alkyl, —ON(C₁₋₆ alkyl)₂, —N(C₁₋₆ alkyl)₂,—N(C₁₋₆ alkyl)₃ ⁺X⁻, —NH(C₁₋₆ alkyl)₂ ⁺X⁻, —NH₂(C₁₋₆ alkyl) ⁺X⁻, —NH₃⁺X⁻, —N(OC₁₋₆ alkyl)(C₁₋₆ alkyl), —N(OH)(C₁₋₆ alkyl), —NH(OH), —SH,—SC₁₋₆ alkyl, —SS(C₁₋₆ alkyl), —C(═O)(C₁₋₆ alkyl), —CO₂H, —O₂(C₁₋₆alkyl), —OC(═O)(C₁₋₆ alkyl), —OCO₂(C₁₋₆ alkyl), —C(═O)NH₂, —C(═O)N(C₁₋₆alkyl)₂, —OC(═O)NH(C₁₋₆ alkyl), —NHC(═O)(C₁₋₆ alkyl), —N(C₁₋₆alkyl)C(═O)(C₁₋₆ alkyl), —NHCO₂(C₁₋₆ alkyl), —NHC(═O)N(C₁₋₆ alkyl)₂,—NHC(═O)NH(C₁₋₆ alkyl), —NHC(═O)NH₂, —C(═NH)O(C₁₋₆ alkyl), —OC(═NH)(C₁₋₆alkyl), —OC(═NH)OC₁₋₆ alkyl, —C(═NH)N(C₁₋₆ alkyl)₂, —C(═NH)NH(C₁₋₆alkyl), —C(═NH)NH₂, —OC(═NH)N(C₁₋₆ alkyl)₂, —OC(NH)NH(C₁₋₆ alkyl),—OC(NH)NH₂, —NHC(NH)N(C₁₋₆ alkyl)₂, —NHC(═NH)NH₂, —NHSO₂(C₁₋₆ alkyl),—SO₂N(C₁₋₆ alkyl)₂, —SO₂NH(C₁₋₆ alkyl), —SO₂NH₂, —SO₂C₁₋₆ alkyl,—SO₂OC₁₋₆ alkyl, —OSO₂C₁₋₆ alkyl, —SOC₁₋₆ alkyl, —Si(C₁₋₆ alkyl)₃,—OSi(C₁₋₆ alkyl)₃—C(═S)N(C₁₋₆ alkyl)₂, C(═S)NH(C₁₋₆ alkyl), C(═S)NH₂,—C(═O)S(C₁₋₆ alkyl), —C(═S)SC₁₋₆ alkyl, —SC(═S)SC₁₋₆ alkyl, —P(═O)₂(C₁₋₆alkyl), —P(═O)(C₁₋₆ alkyl)₂, —OP(═O)(C₁₋₆ alkyl)₂, —OP(═O)(OC₁₋₆alkyl)₂, C₁₋₆ alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl,C₃₋₁₀ carbocyclyl, C₆₋₁₀ aryl, 3-10 membered heterocyclyl, 5-10 memberedheteroaryl; or two geminal R^(gg) substituents can be joined to form ═Oor ═S; wherein X⁻ is a counterion.

A “counterion” or “anionic counterion” is a negatively charged groupassociated with a cationic quaternary amino group in order to maintainelectronic neutrality. Exemplary counterions include halide ions (e.g.,F, Cl, Br, I), NO₃, ClO₄, OH, H₂PO₄, HSO₄, sulfonate ions (e.g.,methansulfonate, trifluoromethanesulfonate, p-toluenesulfonate,benzenesulfonate, 10-camphor sulfonate, naphthalene-2-sulfonate,naphthalene-1-sulfonic acid-5-sulfonate, ethan-1-sulfonicacid-2-sulfonate, and the like), and carboxylate ions (e.g., acetate,ethanoate, propanoate, benzoate, glycerate, lactate, tartrate,glycolate, and the like).

“Halo” or “halogen” refers to fluorine (fluoro, —F), chlorine (chloro,—Cl), bromine (bromo, —Br), or iodine (iodo, —I).

“Acyl” as used herein refers to a moiety selected from the groupconsisting of —C(═O)R^(aa), —CHO, —CO₂R^(aa), —C(═O)N(R^(bb))₂,—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂,—C(═O)NR^(bb)SO₂R^(aa), —C(═S)N(R^(bb))₂, —C(═O)SR^(aa), or—C(═S)SR^(aa), wherein R^(aa) and R^(bb) are as defined herein.

Nitrogen atoms can be substituted or unsubstituted as valency permits,and include primary, secondary, tertiary, and quarternary nitrogenatoms. Exemplary nitrogen atom substitutents include, but are notlimited to, hydrogen, —OH, —OR^(aa), —N(R^(cc))₂, —CN, —C(═O)R^(aa),—C(═O)N(R^(cc))₂, —CO₂R^(aa), —SO₂R^(aa), —C(═NR^(bb))R^(aa),—C(═NR^(cc))OR^(aa), —C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂, —SO₂R^(cc),—SO₂OR^(cc), —SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc), —C(═S)SR^(cc),—P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)₂N(R^(cc))₂, —P(═O)(NR^(cc))₂,C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 memberedheteroaryl, or two R^(cc) groups attached to a nitrogen atom are joinedto form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring,wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl,and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5R^(dd) groups, and wherein R^(aa), R^(bb), R^(cc), and R^(dd) are asdefined above.

In certain embodiments, the substituent present on a nitrogen atom is anitrogen protecting group (also referred to as an amino protectinggroup). Nitrogen protecting groups include, but are not limited to, —OH,—OR^(aa), —N(R^(cc))₂, —C(═O)R^(aa), —C(═O)N(R^(cc))₂, —CO₂R^(aa),—SO₂R^(aa), —C(═NR^(cc))R^(aa), —C(═NR^(cc))OR^(aa),—C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂, —SO₂R^(cc), —SO₂OR^(cc),—SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc), —C(═S)SR^(cc), C₁₋₁₀ alkyl(e.g., aralkyl, heteroaralkyl), C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 memberedheteroaryl groups, wherein each alkyl, alkenyl, alkynyl, carbocyclyl,heterocyclyl, aralkyl, aryl, and heteroaryl is independently substitutedwith 0, 1, 2, 3, 4, or 5 R^(dd) groups, and wherein R^(aa), R^(bb),R^(cc) and R^(dd) are as defined herein. Nitrogen protecting groups arewell known in the art and include those described in detail inProtecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts,3^(rd) edition, John Wiley & Sons, 1999, incorporated herein byreference.

For example, nitrogen protecting groups such as amide groups (e.g.,—C(═O)R^(aa)) include, but are not limited to, formamide, acetamide,chloroacetamide, trichloroacetamide, trifluoroacetamide,phenylacetamide, 3-phenylpropanamide, picolinamide,3-pyridylcarboxamide, N-benzoylphenylalanyl derivative, benzamide,p-phenylbenzamide, o-nitophenylacetamide, o-nitrophenoxyacetamide,acetoacetamide, (N′-dithiobenzyloxyacylamino)acetamide,3-(p-hydroxyphenyl)propanamide, 3-(o-nitrophenyl)propanamide,2methyl-2(o-nitrophenoxy)propanamide,2-methyl-2-(o-phenylazophenoxy)propanamide, 4-chlorobutanamide,3-methyl-3-nitrobutanamide, o-nitrocinnamide, N-acetylmethioninederivative, o-nitrobenzamide, and o-(benzoyloxymethyl)benzamide.

Nitrogen protecting groups such as carbamate groups (e.g.,—C(═O)OR^(aa)) include, but are not limited to, methyl carbamate, ethylcarbamante, 9-fluorenylmethyl carbamate (Fmoc),9-(2-sulfo)fluorenylmethyl carbamate, 9-(2,7-dibromo)fluoroenylmethylcarbamate,2,7-di-t-butyl-[9-(10,10-dioxo-10,10,10,10-tetrahydrothioxanthyl)]methylcarbamate (DBD-Tmoc), 4-methoxyphenacyl carbamate (Phenoc),2,2,2-trichloroethyl carbamate (Troc), 2-trimethylsilylethyl carbamate(Teoc), 2-phenylethyl carbamate (hZ), 1-(1-adamantyl)-1-methylethylcarbamate (Adpoc), 1,1-dimethyl-2-haloethyl carbamate,1,1-dimethyl-2,2-dibromoethyl carbamate (DB-t-BOC),1,1-dimethyl-2,2,2-trichloroethyl carbamate (TCBOC),1-methyl-1-(4-biphenylyl)ethyl carbamate (Bpoc),1-(3,5-di-t-butylphenyl)-1-methylethyl carbamate (t-Bumeoc), 2-(2′- and4′-pyridyl)ethyl carbamate (Pyoc), 2-(N,N-dicyclohexylcarboxamido)ethylcarbamate, t-butyl carbamate (BOC), 1-adamantyl carbamate (Adoc), vinylcarbamate (Voc), allyl carbamate (Alloc), 1-isopropylallyl carbamate(Ipaoc), cinnamyl carbamate (Coc), 4-nitrocinnamyl carbamate (Noc),8-quinolyl carbamate, N-hydroxypiperidinyl carbamate, alkyldithiocarbamate, benzyl carbamate (Cbz), p-methoxybenzyl carbamate (Moz),p-nitobenzyl carbamate, p-bromobenzyl carbamate, p-chlorobenzylcarbamate, 2,4-dichlorobenzyl carbamate, 4-methylsulfinylbenzylcarbamate (Msz), 9-anthrylmethyl carbamate, diphenylmethyl carbamate,2-methylthioethyl carbamate, 2-methylsulfonylethyl carbamate,2-(p-toluenesulfonyl)ethyl carbamate, [2-(1,3-dithianyl)]methylcarbamate (Dmoc), 4-methylthiophenyl carbamate (Mtpc),2,4-dimethylthiophenyl carbamate (Bmpc), 2-phosphonioethyl carbamate(Peoc), 2-triphenylphosphonioisopropyl carbamate (Ppoc),1,1-dimethyl-2-cyanoethyl carbamate, m-chloro-p-acyloxybenzyl carbamate,p-(dihydroxyboryl)benzyl carbamate, 5-benzisoxazolylmethyl carbamate,2-(trifluoromethyl)-6-chromonylmethyl carbamate (Tcroc), m-nitrophenylcarbamate, 3,5dimethoxybenzyl carbamate, o-nitrobenzyl carbamate,3,4-dimethoxy-6-nitrobenzyl carbamate, phenyl(o-nitrophenyl)methylcarbamate, t-amyl carbamate, S-benzyl thiocarbamate, p-cyanobenzylcarbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentylcarbamate, cyclopropylmethyl carbamate, p-decyloxybenzyl carbamate,2,2-dimethoxyacylvinyl carbamate, o-(N,N-dimethylcarboxamido)benzylcarbamate, 1,1-dimethyl-3-(N,N-dimethylcarboxamido)propyl carbamate,1,1-dimethylpropynyl carbamate, di(2-pyridyl)methyl carbamate,2-furanylmethyl carbamate, 2-iodoethyl carbamate, isoborynl carbamate,isobutyl carbamate, isonicotinyl carbamate,p-(p′-methoxyphenylazo)benzyl carbamate, 1-methylcyclobutyl carbamate,1-methylcyclohexyl carbamate, 1-methyl-1-cyclopropylmethyl carbamate,1-methyl-1-(3,5-dimethoxyphenyl)ethyl carbamate,1-methyl-1-(p-phenylazophenyl)ethyl carbamate, 1-methyl-1-phenylethylcarbamate, 1-methyl-1-(4-pyridyl)ethyl carbamate, phenyl carbamate,p-(phenylazo)benzyl carbamate, 2,4,6-tri-t-butylphenyl carbamate,4-(trimethylammonium)benzyl carbamate, and 2,4,6-trimethylbenzylcarbamate.

Nitrogen protecting groups such as sulfonamide groups (e.g.,—S(═O)₂R^(aa)) include, but are not limited to, p-toluenesulfonamide(Ts), benzenesulfonamide, 2,3,6,-trimethyl-4-methoxybenzenesulfonamide(Mtr), 2,4,6-trimethoxybenzenesulfonamide (Mtb),2,6-dimethyl-4-methoxybenzenesulfonamide (Pme),2,3,5,6-tetramethyl-4-methoxybenzenesulfonamide (Mte),4-methoxybenzenesulfonamide (Mbs), 2,4,6-trimethylbenzenesulfonamide(Mts), 2,6-dimethoxy-4-methylbenzenesulfonamide (iMds),2,2,5,7,8-pentamethylchroman-6-sulfonamide (Pmc), methanesulfonamide(Ms), β-trimethylsilylethanesulfonamide (SES), 9-anthracenesulfonamide,4-(4′,8′-dimethoxynaphthylmethyl)benzenesulfonamide (DNMBS),benzylsulfonamide, trifluoromethylsulfonamide, and phenacylsulfonamide.

Other nitrogen protecting groups include, but are not limited to,benzoyl (Bz), phenothiazinyl-(10)-acyl derivative,N′-p-toluenesulfonylaminoacyl derivative, N′-phenylaminothioacylderivative, N-benzoylphenylalanyl derivative, N-acetylmethioninederivative, 4,5-diphenyl-3-oxazolin-2-one, N-phthalimide,N-dithiasuccinimide (Dts), N-2,3-diphenylmaleimide,N-2,5-dimethylpyrrole, N-1,1,4,4-tetramethyldisilylazacyclopentaneadduct (STABASE), 5-substituted1,3-dimethyl-1,3,5-triazacyclohexan-2-one, 5-substituted1,3-dibenzyl-1,3,5-triazacyclohexan-2-one, 1-substituted3,5-dinitro-4-pyridone, N-methylamine, N-allylamine,N-[2-(trimethylsilyl)ethoxy]methylamine (SEM), N-3-acetoxypropylamine,N-(1-isopropyl-4-nitro-2-oxo-3-pyroolin-3-yl)amine, quaternary ammoniumsalts, N-benzylamine, N-di(4-methoxyphenyl)methylamine,N-5-dibenzosuberylamine, N-triphenylmethylamine (Tr),N-[(4-methoxyphenyl)diphenylmethyl]amine (MMTr),N-9-phenylfluorenylamine (PhF),N-2,7-dichloro-9-fluorenylmethyleneamine, N-ferrocenylmethylamino (Fcm),N-2-picolylamino N′-oxide, N-1,1-dimethylthiomethyleneamine,N-benzylideneamine, N-p-methoxybenzylideneamine,N-diphenylmethyleneamine, N-[(2-pyridyl)mesityl]methyleneamine,N-(N′,N′-dimethylaminomethylene)amine, N,N′-isopropylidenediamine,N-p-nitrobenzylideneamine, N-salicylideneamine,N-5-chlorosalicylideneamine,N-(5-chloro-2-hydroxyphenyl)phenylmethyleneamine,N-cyclohexylideneamine, N-(5,5-dimethyl-3-oxo-1-cyclohexenyl)amine,N-borane derivative, N-diphenylborinic acid derivative,N-[phenyl(pentaacylchromium- or tungsten)acyl]amine, N-copper chelate,N-zinc chelate, N-nitroamine, N-nitrosoamine, amine N-oxide,diphenylphosphinamide (Dpp), dimethylthiophosphinamide (Mpt),diphenylthiophosphinamide (Ppt), dialkyl phosphoramidates, dibenzylphosphoramidate, diphenyl phosphoramidate, benzenesulfenamide,o-nitrobenzenesulfenamide (Nps), 2,4-dinitrobenzenesulfenamide,pentachlorobenzenesulfenamide, 2-nitro-4-methoxybenzenesulfenamide,triphenylmethylsulfenamide, and 3nitropyridinesulfenamide (Npys).

In certain embodiments, the substituent present on an oxygen atom is anoxygen protecting group (also referred to as a hydroxyl protectinggroup). Oxygen protecting groups include, but are not limited to,—R^(aa), —N(R^(bb))₂, —C(═O)SR^(aa), —C(═O)R^(aa), —CO₂R^(aa),—C(═O)N(R^(bb))₂, —C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa),—C(═NR^(bb))N(R^(bb))₂, —S(═O)R^(aa), —SO₂R^(aa), —Si(R^(aa))₃,—P(R^(cc))₂, —P(R^(cc))₃, —P(═O)₂R^(aa), —P(═O)(R^(aa))₂,—P(═O)(OR^(cc))₂, —P(═O)₂N(R^(bb))₂, and —P(═O)(NR^(bb))₂, whereinR^(aa), R^(bb), and R^(cc) are as defined herein. Oxygen protectinggroups are well known in the art and include those described in detailin Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M.Wuts, 3^(rd) edition, John Wiley & Sons, 1999, incorporated herein byreference.

Exemplary oxygen protecting groups include, but are not limited to,methyl, methoxylmethyl (MOM), methylthiomethyl (MTM), t-butylthiomethyl,(phenyldimethylsilyl)methoxymethyl (SMOM), benzyloxymethyl (BOM),p-methoxybenzyloxymethyl (PMBM), (4-methoxyphenoxy)methyl (p-AOM),guaiacolmethyl (GUM), t-butoxymethyl, 4-pentenyloxymethyl (POM),siloxymethyl, 2-methoxyethoxymethyl (MEM), 2,2,2-trichloroethoxymethyl,bis(2-chloroethoxy)methyl, 2-(trimethylsilyl)ethoxymethyl (SEMOR),tetrahydropyranyl (THP), 3-bromotetrahydropyranyl,tetrahydrothiopyranyl, 1-methoxycyclohexyl, 4-methoxytetrahydropyranyl(MTHP), 4-methoxytetrahydrothiopyranyl, 4-methoxytetrahydrothiopyranylS,S-dioxide, 1-[(2-chloro-4-methyl)phenyl]-4-methoxypiperidin-4-yl(CTMP), 1,4-dioxan-2-yl, tetrahydrofuranyl, tetrahydrothiofuranyl,2,3,3a,4,5,6,7,7a-octahydro-7,8,8-trimethyl-4,7-methanobenzofuran-2-yl,1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 1-methyl-1-methoxyethyl,1-methyl-1-benzyloxyethyl, 1-methyl-1-benzyloxy-2-fluoroethyl,2,2,2-trichloroethyl, 2-trimethylsilylethyl, 2-(phenylselenyl)ethyl,t-butyl, allyl, p-chlorophenyl, p-methoxyphenyl, 2,4-dinitrophenyl,benzyl (Bn), p-methoxybenzyl, 3,4-dimethoxybenzyl, o-nitrobenzyl,p-nitrobenzyl, p-halobenzyl, 2,6-dichlorobenzyl, p-cyanobenzyl,p-phenylbenzyl, 2picolyl, 4-picolyl, 3-methyl-2-picolyl N-oxido,diphenylmethyl, p,p′-dinitrobenzhydryl, 5-dibenzosuberyl,triphenylmethyl, α-naphthyldiphenylmethyl,p-methoxyphenyldiphenylmethyl, di(p-methoxyphenyl)phenylmethyl,tri(p-methoxyphenyl)methyl, 4-(4′-bromophenacyloxyphenyl)diphenylmethyl,4,4′,4″-tris(4,5-dichlorophthalimidophenyl)methyl,4,4′,4″-tris(levulinoyloxyphenyl)methyl,4,4′,4″-tris(benzoyloxyphenyl)methyl,3-(imidazol-1-yl)bis(4′,4″-dimethoxyphenyl)methyl,1,1-bis(4-methoxyphenyl)-1′-pyrenylmethyl, 9-anthryl,9-(9-phenyl)xanthenyl, 9-(9-phenyl-10-oxo)anthryl,1,3-benzodisulfuran-2-yl, benzisothiazolyl S,S-dioxido, trimethylsilyl(TMS), triethylsilyl (TES), triisopropylsilyl (TIPS),dimethylisopropylsilyl (IPDMS), diethylisopropylsilyl (DEIPS),dimethylthexylsilyl, t-butyldimethylsilyl (TBDMS), t-butyldiphenylsilyl(TBDPS), tribenzylsilyl, tri-p-xylylsilyl, triphenylsilyl,diphenylmethylsilyl (DPMS), t-butylmethoxyphenylsilyl (TBMPS), formate,benzoylformate, acetate, chloroacetate, dichloroacetate,trichloroacetate, trifluoroacetate, methoxyacetate,triphenylmethoxyacetate, phenoxyacetate, p-chlorophenoxyacetate,3-phenylpropionate, 4-oxopentanoate (levulinate),4,4-(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate,adamantoate, crotonate, 4-methoxycrotonate, benzoate, p-phenylbenzoate,2,4,6-trimethylbenzoate (mesitoate), alkyl methyl carbonate,9-fluorenylmethyl carbonate (Fmoc), alkyl ethyl carbonate, alkyl2,2,2-trichloroethyl carbonate (Troc), 2-(trimethylsilyl)ethyl carbonate(TMSEC), 2-(phenylsulfonyl) ethyl carbonate (Psec),2-(triphenylphosphonio) ethyl carbonate (Peoc), alkyl isobutylcarbonate, alkyl vinyl carbonate alkyl allyl carbonate, alkylp-nitrophenyl carbonate, alkyl benzyl carbonate, alkyl p-methoxybenzylcarbonate, alkyl 3,4-dimethoxybenzyl carbonate, alkyl o-nitrobenzylcarbonate, alkyl p-nitrobenzyl carbonate, alkyl S-benzyl thiocarbonate,4-ethoxy1-napththyl carbonate, methyl dithiocarbonate, 2-iodobenzoate,4-azidobutyrate, 4-nitro-4-methylpentanoate, o-(dibromomethyl)benzoate,2-formylbenzenesulfonate, 2-(methylthiomethoxy)ethyl,4-(methylthiomethoxy)butyrate, 2-(methylthiomethoxymethyl)benzoate,2,6-dichloro-4-methylphenoxyacetate,2,6-dichloro-4-(1,1,3,3-tetramethylbutyl)phenoxyacetate,2,4-bis(1,1-dimethylpropyl)phenoxyacetate, chlorodiphenylacetate,isobutyrate, monosuccinoate, (E)-2-methyl-2butenoate,o-(methoxyacyl)benzoate, α-naphthoate, nitrate, alkylN,N,N′,N′-tetramethylphosphorodiamidate, alkyl N-phenylcarbamate,borate, dimethylphosphinothioyl, alkyl 2,4-dinitrophenylsulfenate,sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate(Ts).

In certain embodiments, the substituent present on an sulfur atom is ansulfur protecting group (also referred to as a thiol protecting group).Sulfur protecting groups include, but are not limited to, —R^(aa),—N(R^(bb))₂, —C(═O)SR^(aa), —C(═O)R^(aa), —CO₂R^(aa), —C(═O)N(R^(bb))₂,—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂,—S(═O)R^(aa), —SO₂R^(aa), —Si(R^(aa))₃, —P(R^(cc))₂, —P(R^(cc))₃,—P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)(OR^(cc))₂, —P(═O)₂N(R^(bb))₂, and—P(═O)(NR^(bb))₂, wherein R^(aa), R^(bb), and R^(cc) are as definedherein. Sulfur protecting groups are well known in the art and includethose described in detail in Protecting Groups in Organic Synthesis, T.W. Greene and P. G. M. Wuts, 3^(rd) edition, John Wiley & Sons, 1999,incorporated herein by reference.

As used herein, the term “leaving group” is given its ordinary meaningin the art of synthetic organic chemistry and refers to an atom or agroup capable of being displaced by a nucleophile. Examples of suitableleaving groups include, but are not limited to, halogen (such as F, Cl,Br, or I (iodine)), alkoxycarbonyloxy, aryloxycarbonyloxy,alkanesulfonyloxy, arenesulfonyloxy, alkyl-carbonyloxy (e.g., acetoxy),arylcarbonyloxy, aryloxy, methoxy, N,O-dimethylhydroxylamino, pixyl, andhaloformates. In some cases, the leaving group is a sulfonic acid ester,such as toluenesulfonate (tosylate, —OTs), methanesulfonate (mesylate,—OMs), p-bromobenzenesulfonyloxy (brosylate, —OBs), ortrifluoromethanesulfonate (triflate, —OTf). In some cases, the leavinggroup is a brosylate, such as p-bromobenzenesulfonyloxy. In some cases,the leaving group is a nosylate, such as 2-nitrobenzenesulfonyloxy. Insome embodiments, the leaving group is a sulfonate-containing group. Insome embodiments, the leaving group is a tosylate group. The leavinggroup may also be a phosphineoxide (e.g., formed during a Mitsunobureaction) or an internal leaving group such as an epoxide or cyclicsulfate. Other non-limiting examples of leaving groups are water,ammonia, alcohols, ether moieties, thioether moieties, zinc halides,magnesium moieties, diazonium salts, and copper moieties.

These and other exemplary substituents are described in more detail inthe Detailed Description, Figures, Examples, and claims. The inventionis not intended to be limited in any manner by the above exemplarylisting of substituents.

Other Definitions

The following definitions are more general terms used throughout thepresent application:

As used herein, the term “pharmaceutically acceptable salt” refers tothose salts which are, within the scope of sound medical judgment,suitable for use in contact with the tissues of humans and lower animalswithout undue toxicity, irritation, allergic response and the like, andare commensurate with a reasonable benefit/risk ratio. Pharmaceuticallyacceptable salts are well known in the art. For example, Berge et al.,describe pharmaceutically acceptable salts in detail in J.Pharmaceutical Sciences, 1977, 66, 1-19, incorporated herein byreference. Pharmaceutically acceptable salts of the compounds of thisinvention include those derived from suitable inorganic and organicacids and bases. Examples of pharmaceutically acceptable, nontoxic acidaddition salts are salts of an amino group formed with inorganic acidssuch as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuricacid, and perchloric acid or with organic acids such as acetic acid,oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, ormalonic acid or by using other methods known in the art such as ionexchange. Other pharmaceutically acceptable salts include adipate,alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate,borate, butyrate, camphorate, camphorsulfonate, citrate,cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate,formate, fumarate, glucoheptonate, glycerophosphate, gluconate,hemisulfate, heptanoate, hexanoate, hydroiodide,2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, laurylsulfate, malate, maleate, malonate, methanesulfonate,2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate,pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate,pivalate, propionate, stearate, succinate, sulfate, tartrate,thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and thelike. Salts derived from appropriate bases include alkali metal,alkaline earth metal, ammonium and N+(C₁₋₄ alkyl)₄ salts. Representativealkali or alkaline earth metal salts include sodium, lithium, potassium,calcium, magnesium, and the like. Further pharmaceutically acceptablesalts include, when appropriate, nontoxic ammonium, quaternary ammonium,and amine cations formed using counterions such as halide, hydroxide,carboxylate, sulfate, phosphate, nitrate, loweralkyl sulfonate, and arylsulfonate.

“Solvate” refers to forms of the compound that are associated with asolvent or water (also referred to as “hydrate”), usually by asolvolysis reaction. This physical association includes hydrogenbonding. Conventional solvents include water, ethanol, acetic acid andthe like. The compounds of the invention may be prepared e.g. incrystalline form and may be solvated or hydrated. Suitable solvatesinclude pharmaceutically acceptable solvates, such as hydrates, andfurther include both stoichiometric solvates and non-stoichiometricsolvates. In certain instances the solvate will be capable of isolation,for example when one or more solvent molecules are incorporated in thecrystal lattice of the crystalline solid. “Solvate” encompasses bothsolution-phase and isolable solvates. Representative solvates includehydrates, ethanolates and methanolates.

“Tautomers” refer to compounds that are interchangeable forms of aparticular compound structure, and that vary in the displacement ofhydrogen atoms and electrons. Thus, two structures may be in equilibriumthrough the movement of it electrons and an atom (usually H). Forexample, enols and ketones are tautomers because they are rapidlyinterconverted by treatment with either acid or base. Another example oftautomerism is the aci- and nitro- forms of phenylnitromethane, that arelikewise formed by treatment with acid or base. Tautomeric forms may berelevant to the attainment of the optimal chemical reactivity andbiological activity of a compound of interest.

It is also to be understood that compounds that have the same molecularformula but differ in the nature or sequence of bonding of their atomsor the arrangement of their atoms in space are termed “isomers”. Isomersthat differ in the arrangement of their atoms in space are termed“stereoisomers”.

Stereoisomers that are not mirror images of one another are termed“diastereomers” and those that are non-superimposable mirror images ofeach other are termed “enantiomers”. When a compound has an asymmetriccenter, for example, it is bonded to four different groups, a pair ofenantiomers is possible. An enantiomer can be characterized by theabsolute configuration of its asymmetric center and is described by theR- and S-sequencing rules of Cahn and Prelog, or by the manner in whichthe molecule rotates the plane of polarized light and designated asdextrorotatory or levorotatory (i.e., as (+) or (−)-isomersrespectively). A chiral compound can exist as either individualenantiomer or as a mixture thereof. A mixture containing equalproportions of the enantiomers is called a “racemic mixture”.

“Prodrugs” refers to compounds, including derivatives of the compoundsof the invention,which have cleavable groups and become by solvolysis orunder physiological conditions the compounds of the invention which arepharmaceutically active in vivo. Such examples include, but are notlimited to, choline ester derivatives and the like, N-alkylmorpholineesters and the like. Other derivatives of the compounds of thisinvention have activity in both their acid and acid derivative forms,but in the acid sensitive form often offers advantages of solubility,tissue compatibility, or delayed release in the mammalian organism (see,Bundgard, H., Design of Prodrugs, pp. 7-9, 21-24, Elsevier, Amsterdam1985). Prodrugs include acid derivatives well know to practitioners ofthe art, such as, for example, esters prepared by reaction of the parentacid with a suitable alcohol, or amides prepared by reaction of theparent acid compound with a substituted or unsubstituted amine, or acidanhydrides, or mixed anhydrides. Simple aliphatic or aromatic esters,amides and anhydrides derived from acidic groups pendant on thecompounds of this invention are particular prodrugs. In some cases it isdesirable to prepare double ester type prodrugs such as (acyloxy)alkylesters or ((alkoxycarbonyl)oxy)alkylesters. Particularly the C₁ to C₈alkyl, C₂-C₈ alkenyl, C₂-C₈ alkynyl, aryl, C₇-C₁₂ substituted aryl, andC₇-C₁₂ arylalkyl esters of the compounds of the invention.

A “subject” to which administration is contemplated includes, but is notlimited to, humans (i.e., a male or female of any age group, e.g., apediatric subject (e.g, infant, child, adolescent) or adult subject(e.g., young adult, middleaged adult, or senior adult)) and/or othernonhuman animals, for example, mammals (e.g., primates (e.g., cynomolgusmonkeys, rhesus monkeys); commercially relevant mammals such as cattle,pigs, horses, sheep, goats, cats, and/or dogs) and birds (e.g.,commercially relevant birds such as chickens, ducks, geese, and/orturkeys). In certain embodiments, the animal is a mammal. The animal maybe a male or female and at any stage of development. A nonhuman animalmay be a transgenic animal, such as a transgenic mouse or transgenicpig.

The term “biological sample” refers to any sample including tissuesamples (such as tissue sections and needle biopsies of a tissue); cellsamples (e.g., cytological smears (such as Pap or blood smears) orsamples of cells obtained by microdissection); samples of wholeorganisms (such as samples of yeasts or bacteria); or cell fractions,fragments or organelles (such as obtained by lysing cells and separatingthe components thereof by centrifugation or otherwise). Other examplesof biological samples include blood, serum, urine, semen, fecal matter,cerebrospinal fluid, interstitial fluid, mucus, tears, sweat, pus,biopsied tissue (e.g., obtained by a surgical biopsy or needle biopsy),nipple aspirates, milk, vaginal fluid, saliva, swabs (such as buccalswabs), or any material containing biomolecules that is derived from afirst biological sample. Biological samples also include thosebiological samples that are transgenic, such as transgenic oocyte, spermcell, blastocyst, embryo, fetus, donor cell, or cell nucleus.

“Treat,” “treating,” and “treatment” contemplate an action that occurswhile a subject is suffering from a condition and that reduces theseverity of the condition or retards or slows the progression of thecondition (“therapeutic treatment”), and also contemplates an actionthat occurs before a subject begins to suffer from the condition andthat inhibits or reduces the severity of the condition (“prophylactictreatment”).

As used herein, “condition,” “disease,” and “disorder” are usedinterchangeably.

An “effective amount” of a compound of the present invention refers toan amount sufficient to elicit the desired biological response, i.e.,treating the condition. As will be appreciated by those of ordinaryskill in this art, the effective amount of a compound of the inventionmay vary depending on such factors as the desired biological endpoint,the pharmacokinetics of the compound, the condition being treated, themode of administration, and the age and health of the subject. Aneffective amount encompasses therapeutic and prophylactic treatment. Forexample, in treating cancer, an effective amount of an inventivecompound may reduce the tumor burden or stop the growth or spread of atumor.

A “therapeutically effective amount” of a compound of the presentinvention is an amount sufficient to provide a therapeutic benefit inthe treatment of a condition or to delay or minimize one or moresymptoms associated with the condition. A therapeutically effectiveamount of a compound means an amount of therapeutic agent, alone or incombination with other therapies, which provides a therapeutic benefitin the treatment of the condition. The term “therapeutically effectiveamount” can encompass an amount that improves overall therapy, reducesor avoids symptoms or causes of the condition, or enhances thetherapeutic efficacy of another therapeutic agent.

A “prophylactically effective amount” of a compound of the presentinvention is an amount sufficient to prevent a condition, or one or moresymptoms associated with the condition or prevent its recurrence. Aprophylactically effective amount of a compound means an amount of atherapeutic agent, alone or in combination with other agents, whichprovides a prophylactic benefit in the prevention of the condition. Theterm “prophylactically effective amount” can encompass an amount thatimproves overall prophylaxis or enhances the prophylactic efficacy ofanother prophylactic agent.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 (FIG. 1) includes the chemical structures of representative JNKinhibitors.

FIGS. 2A and 2B (FIGS. 2A and 2B) depict the crystal structure (PDB ID1T46) of c-Kit (ribbons) complexed with imatinib (sticks) (FIG. 2A), andthe crystal structure (PDB ID 1XBB) of Syk (ribbons) complexed withimatinib (sticks) (FIG. 2B).

FIG. 3 (FIG. 3) shows the chemical structures of JNK inhibitors JNK-IN-5to 12.

FIG. 4 (FIG. 4) depicts a docking result of JNK-IN-7 (sticks) with JNK3(ribbons). Potential hydrogen-bonding interactions are indicated withdashed lines.

FIGS. 5A to 5C (FIGS. 5A to 5C) show the mass spectra obtained fromanalysis of untreated (FIG. 5A) or JNK-IN-7 treated (FIG. 5B)recombinant JNK3 kinase domain, and the HCD MS/MS spectrum of thepeptide LMDANLC*QVIQME (JNK residues 148-160; C* indicates a labeledcysteine residue) (FIG. 5C). Identification of ions of type b and y areindicated with lines above and below the sequence, respectively.

FIG. 6 (FIG. 6) depicts the crystal structure of JNK3 residues 39-402modified at Cys-154 by JNK-IN-7. The covalent inhibitors and the keyresidues of JNK3 that are involved in hydrophobic and hydrogen bondinginteractions with the covalent inhibitors are labeled and are shown instick models. The hydrogen bonds between the kinase “hinge” residueMet-149 and the aminopyrimidine-motif of the covalent inhibitors arerepresented as dotted lines.

FIG. 7 (FIG. 7) is a 2Fo-Fc electron density map corresponding to thecovalent inhibitor JNK-IN-7 (sticks). The map is contoured at la andshows unambiguous electron densities of JNK-IN-7.

FIG. 8 (FIG. 8) shows the kinetics of labeling of JNK in JNK-IN-5, anirreversible JNK inhibitor, compared with JNK-IN-6, a reversibleinhibitor. A375 cells were incubated with inhibitors for the indicatedamount of time after which cell lysates were prepared and labeled withATP-biotin. Biotinylated proteins were pulled down with streptavidinbeads and material bound to the beads was eluted and separate bySDS-PAGE followed by Western blot analysis for JNK. Complete protectionof JNK was achieved following a three-hour incubation with JNK-IN-5while no protection of JNK labeling was achieved following incubationwith JNK-IN-6.

FIG. 9 (FIG. 9) illustrates the cellular kinase selectivity as assessedusing the KiNativ™ technology. Percent inhibition of kinase labeling byATP-biotin that results from incubating A375 cells with the inhibitorsfor 3 hours at a concentration of 1 μM is indicated (larger numbersindicate stronger binding to the kinase).

FIG. 10 (FIG. 10) shows the sequence alignment of kinases that possess apotentially reactive cysteine (highlighted) that is at least fiveresidues N- and C-terminal to C154 of JNK3. Kinase sequences wereretrieved from the human KinBase, and kinome-wide sequence alignment wasperformed with ClustalX. The gatekeeper amino acid residues are alsohighlighted.

FIG. 11 (FIG. 11) shows the Kinome Scan™ (DiscoverRx) profiles for theirreversible JNK inhibitors.

FIG. 12 (FIG. 12) shows the enzymatic IC₅₀'s or dissociation constants(K_(d)) for the potential additional kinase targets. For JNK-IN-7 andJNK-IN-11, the kinases with the score below 5 were tested; and forJNK-IN-8 and JNK-IN-12, kinases with score below 1 were tested. Scoreswere obtained from the profiling against a 400 kinase panel using KinomeScan™ technology as illustrated in FIG. 11.

FIG. 13 (FIG. 13) shows the biochemical IC₅₀ 's for additional kinasetargets selected based upon the result of screening a panel of 105kinases at a concentration of 1 μM (Dundee Kinase panel).

FIGS. 14A to 14H (FIGS. 14A to 14H) illustrate the evaluation of thecellular selectivity for the JNK inhibitors as monitored throughinhibition of phosphorylation of key nodes on multiple signaltransduction pathways. A375 cells were stimulated with anisomycin (FIGS.14A and 14C to 14F), IGF-1 (FIG. 14B), IL-6 (FIG. 14G), and TNF-α (FIG.14H) for sixty minutes. The output of multiple signaling pathways wasmeasured using high throughput microscopy at multiple concentrations offour JNK inhibitors and a control compound specific to each pathway DMSO(FIG. 14A), MK2206 (allosteric Akt inhibitor, Haoyuan Chemexpress Co.,Limited. Hirai, et al., 2010) (FIG. 14B), PD0325901 (allosteric Mekinhibitor, Haoyuan Chemexpress Co., Limited. Barrett, et al., 2008)(FIGS. 14C and 14D), SB239063 (ATP-competitive p38 inhibitor, HaoyuanChemexpress Co., Limited. Underwood et al., 2000) (FIGS. 14E and 14F),KIN001-040 (ATP-competitive JAK1,2,3 inhibitor, Haoyuan Chemexpress Co.,Limited. Thompson et al., 2002) (FIG. 14G), and KIN001-208 (IKKinhibitor VIII, Haoyuan Chemexpress Co., Limited., Murata, et al., 2004)(FIG. 14H).

FIGS. 15A to 15C (FIG. 15A to 15C) show results of a Western blotanalysis of inhibition of JNK, c-Jun, MSK1, and p38 for JNK-IN-7 (FIG.15A), JNK-IN-8 (FIG. 15B), and JNK-IN-11 (FIG. 15C) following anisomycinstimulation of HEK293-IL1R cells.

FIGS. 16A and 16B (FIGS. 16A and 16B) depict Western blot results.Inhibition of phosphorylation of c-Jun is not recovered following“washout” of JNK-IN-8. HEK293-ILR1 cells were treated with JNK-IN-8 forthree hours, followed by extensive washout of inhibitor and stimulatedwith anisomycin for lh after the indicated hours (FIG. 16A). Celllysates were prepared, resolved by SDS-PAGE, and p-c-Jun (Ser63) andp-JNK were monitored by Western blot. FIG. 16B shows the inhibition ofanisomycin-stimulated c-Jun phosphorylation with varying concentrationsand incubation times of JNK-IN-8 in HEK293-ILR1 cells.

FIG. 17 (FIG. 17) shows curves for the determination of K_(m) for ATF2for JNK WT and JNK Cys116Ser.

FIG. 18 (FIG. 18) shows that mutation of the conserved Cys116 to Serincreases the IC₅₀ for inhibition of JNK2 by over 100-fold for JNK-IN-7and JNK-IN-8 but only by approximately 10-fold for JNK-IN-11.

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS OF THE INVENTION

The present invention provides compounds that inhibit a kinase, andpharmaceutical compositions thereof, for the prevention and treatment ofa disease of a subject. In certain embodiments, the compounds inhibitc-Jun-N-terminal kinase (JNK). In certain embodiments, the compoundsirreversibly inhibit JNK. The present invention further provides methodsof using the compounds described herein, e.g., as biological probes tostudy the inhibition of JNK activity, and as therapeutics, e.g., in theprevention and treatment of diseases associated with JNK activity. Incertain embodiments, the diseases include, but are not limited to,proliferative diseases (e.g., cancer and benign neoplasms),neurodegenerative diseases, metabolic disorders, inflammatory diseases,and cardiovascular diseases.

Compounds

In one aspect of the present invention, provided are compounds ofFormula (I):

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,prodrugs, and compositions thereof;wherein:

Ring A is a carbocyclic, heterocyclic, heteroaryl, or aryl ring;

each instance of R^(A) is independently selected from the groupconsisting of hydrogen, halogen, optionally substituted acyl, optionallysubstituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, —OR^(A1), —N(R^(A1))₂, and —SR^(A1), whereineach occurrence of R^(A1) is independently selected from the groupconsisting of hydrogen, acyl, optionally substituted alkyl, optionallysubstituted alkenyl, optionally substituted alkynyl, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, optionally substituted heteroaryl, a nitrogenprotecting group when attached to a nitrogen atom, an oxygen protectinggroup when attached to an oxygen atom, a sulfur protecting group whenattached to a sulfur atom, or two R^(A1) groups are joined to form anoptionally substituted heterocyclic ring;

m is 0, 1, 2, 3, or 4;

Ring B is a group of the formula:

R^(B1) is selected from the group consisting of hydrogen, halogen,optionally substituted acyl, optionally substituted alkyl, optionallysubstituted alkenyl, optionally substituted alkynyl, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, optionally substituted heteroaryl, —OR^(B 1a),N(R^(B1a))₂, and —SR^(B1a), wherein each occurrence of R^(B1a) isindependently selected from the group consisting of hydrogen, acyl,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, a nitrogen protecting group when attached to anitrogen atom, an oxygen protecting group when attached to an oxygenatom, a sulfur protecting group when attached to a sulfur atom, or twoR^(B1a) groups are joined to form an optionally substituted heterocyclicring;

W_(B) is N or CR^(B2), wherein R^(B2) is selected from the groupconsisting of hydrogen, halogen, optionally substituted acyl, optionallysubstituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, —OR^(B2a), —N(R^(B2a))₂, and —SR^(B2a), whereineach occurrence of R^(B2a) is independently selected from the groupconsisting of hydrogen, acyl, optionally substituted alkyl, optionallysubstituted alkenyl, optionally substituted alkynyl, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, optionally substituted heteroaryl, a nitrogenprotecting group when attached to a nitrogen atom, an oxygen protectinggroup when attached to an oxygen atom, a sulfur protecting group whenattached to a sulfur atom, or two R^(B2a) groups are joined to form anoptionally substituted heterocyclic ring;

optionally wherein R^(B1) and R^(B2) are joined to form an optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted heteroaryl, or optionally substituted aryl ring;

Li is a bond directly attaching Ring A to Ring B, or L₁ is ═C(R^(L1a))—,—O—, —S—, —NR^(L1b)—, —NR^(L1b)C(═O)—, —C(═O)NR^(L1b)—, —SC(═O)—,—C(═O)S—, —OC(═O)—, —C(═O)O—, —NR^(L1b)C(═S)—, —C(═S)NR^(L1b)—,trans-CH═CH—, cis-CH═CH—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(L1b)—,—NR^(L1b)S(═O)₂—, or an optionally substituted C₁₋₄ hydrocarbon chain,optionally wherein one methylene unit of the hydrocarbon chain isreplaced with ═C(R^(L1a))—, —O—, —S—, —NR^(L1b)—, —NR^(L1b)C(═O)—,—C(═O)NR^(L1b)—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —O(═O)O—,—NR^(L1b)C(═S)—, —C(═S)NR^(L1b)—, trans-CH═CH—, cis-CH═CH—, —S(═O)₂O—,—OS(═O)₂—, —S(═O)₂NR^(L1b)—, or —NR^(L1b)S(═O)₂—, wherein R^(L1a) ishydrogen, halogen, optionally substituted acyl, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, optionally substituted heteroaryl, —CN, or—NO₂, and R^(L1b) is hydrogen, C₁₋₆ alkyl, or a nitrogen protectinggroup;

represents a single or double bond;

X is an optionally substituted C₁₋₄ hydrocarbon chain, optionallywherein one or more carbon units of the hydrocarbon chain is replacedwith —O—, —S—, or —NR^(X)—, wherein R^(X) is hydrogen, C₁₋₆ alkyl, or anitrogen protecting group;

L₂ is a bond, —O—, —S—, —NR^(L2a)—, —NR^(L2a)C(═O)—, —C(═O)NR^(L2a)—,—SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NR^(L2a)C(═S)—,—C(═S)NR^(L2a)—, trans-CR^(L2b)═CR^(L2b)—, cis-CR^(L2b)═CR^(L2b)—,—C≡C—, —OC(R^(L2b))₂—, —C(R^(L2b))₂O—, —NR^(L2a)C(R^(L2b))₂—,—C(R^(L2b))₂NR^(L2a)—, —SC(R^(L2b))₂—, —C(R^(L2b))₂S—, —S(═O)₂O—,—OS(═O)₂—, —S(═O)₂NR^(L2a)—, —NR^(L2a)S(═O)₂—, or an optionallysubstituted C₁₋₄ hydrocarbon chain, optionally wherein one or morecarbon units of the hydrocarbon chain is replaced with —O—, —S—,—NR^(L2a)—, —NR^(L2a)C(═O)—, —C(═O)NR^(L2a)—, —SC(═O)—, —C(═O)S—,—OC(═O)—, —C(═O)O—, —NR^(L2a)C(═S)—, —C(═S)NR^(L2a)—,trans-CR^(L2b)═CR^(L2b)—, cis-CR^(L2b)═CR^(L2b)—, —C≡C—, —S(═O)₂O—,—OS(═O)₂—, —S(═O)₂NR^(L2a)—, or —NR^(L2a)S(═O)₂—, wherein R^(L2a) ishydrogen, C₁₋₆ alkyl, or a nitrogen protecting group, and wherein eachoccurrence of R^(L2b) is independently selected from the groupconsisting of hydrogen, halogen, optionally substituted alkyl,optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, and optionally substituted heteroaryl, ortwo R^(L2b) groups are joined to form an optionally substitutedcarbocyclic or optionally substituted heterocyclic ring;

each instance of R^(C) is independently selected from the groupconsisting of hydrogen, halogen, optionally substituted acyl, optionallysubstituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, —OR^(C1), —N(R^(C1))₂, and —SR^(C1), whereineach occurrence of R^(C1) is independently selected from the groupconsisting of hydrogen, acyl, optionally substituted alkyl, optionallysubstituted alkenyl, optionally substituted alkynyl, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, optionally substituted heteroaryl, a nitrogenprotecting group when attached to a nitrogen atom, an oxygen protectinggroup when attached to an oxygen atom, a sulfur protecting group whenattached to a sulfur atom, or two R^(C1) groups are joined to form anoptionally substituted heterocyclic ring;

n is 0, 1, 2, 3, or 4;

each instance of R^(D) is independently selected from the groupconsisting of hydrogen, halogen, optionally substituted acyl, optionallysubstituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, —OR^(D1), —N(R^(D1))₂, and —SR^(D1), whereineach occurrence of R^(D1) is independently selected from the groupconsisting of hydrogen, acyl, optionally substituted alkyl, optionallysubstituted alkenyl, optionally substituted alkynyl, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, optionally substituted heteroaryl, a nitrogenprotecting group when attached to a nitrogen atom, an oxygen protectinggroup when attached to an oxygen atom, a sulfur protecting group whenattached to a sulfur atom, or two R^(D1) groups are joined to form anoptionally substituted heterocyclic ring;

p is 0, 1, 2, 3, or 4;

R^(E) is a group of the formula:

wherein:

L₃ is a bond, —O—, —S—, NR^(L3a)—, —NR^(L3a)C(═O)—, —C(═O)NR^(L3a)—,—SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NR^(L3a)C(═S)—,—C(═S)NR^(L3a)—, trans-CR^(L3b)═CR^(L3b)—, cis-CR^(L3b)═CR^(L3b)—,—C≡C—, —OC(R^(L3b))₂—, —C(R^(L3b))₂O—, —NR^(L3a)C(R^(L3b))₂—,—C(R^(L3b))₂NR^(L3a)—, —SC(R^(L3b))₂—, —C(R^(L3b))₂S—, —S(═O)₂O—,—OS(═O)₂—, —S(═O)₂NR^(L3a)—, —NR^(L3a)S(═O)₂—, or an optionallysubstituted C₁₋₄ hydrocarbon chain, optionally wherein one or morecarbon units of the hydrocarbon chain is replaced with —O—, —S—,—NR^(L3a)—, —NR^(L3a)C(═O)—, —C(═O)NR^(L3a)—, —SC(═O)—, —C(═O)S—,—OC(═O)—, —C(═O)O—, —NR^(L3a)C(═S)—, —C(═S)NR^(L3a)—,trans-CR^(L3b)═CR^(L3b)—, cis-CR^(L3b)═CR^(L3b)—, —C≡C—, —S(═O)₂O—,—OS(═O)₂—, —S(═O)₂NR^(L3a)—, or —NR^(L3a)S(═O)₂—, wherein R^(L3a) ishydrogen, C₁₋₆ alkyl, or a nitrogen protecting group, and wherein eachoccurrence of R^(L3b) is independently selected from the groupconsisting of hydrogen, halogen, optionally substituted alkyl,optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, and optionally substituted heteroaryl, ortwo R^(L3b) groups are joined to form an optionally substitutedcarbocyclic or optionally substituted heterocyclic ring;

L₄ is a bond or an optionally substituted C₁₋₄ hydrocarbon chain;

R^(E1) is selected from the group consisting of hydrogen, halogen,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, —CH₂OR^(E1a), —CH₂N(R^(E1a))₂, —CH₂SR^(E1a),—OR^(E1a), —N(R^(E1a))₂, and —SR^(E1a), wherein each occurrence ofR^(E1a) is independently selected from the group consisting of hydrogen,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, and optionallysubstituted heteroaryl, or two R^(E1a) groups are joined to form anoptionally substituted heterocyclic ring;

R^(E2) is selected from the group consisting of hydrogen, halogen,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, —CH₂OR^(E2a), —CH₂N(R^(E2a))₂, —CH₂SR^(E2a),—OR^(E2a), —N(R^(E2a))², and —SR^(E2a), wherein each occurrence ofR^(E2a) is independently selected from the group consisting of hydrogen,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, and optionallysubstituted heteroaryl, or two R^(E2a) groups are joined to form anoptionally substituted heterocyclic ring;

R^(E3) is selected from the group consisting of hydrogen, halogen,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, —CH₂OR^(E3a), CH₂N(R^(E3a))₂, —CH₂SR^(E3a),—OR^(E3a), N(R^(E3a))₂, and —SR^(E3a), wherein each occurrence ofR^(E3a) is independently selected from the group consisting of hydrogen,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, and optionallysubstituted heteroaryl, or two R^(E3a) groups are joined to form anoptionally substituted heterocyclic ring;

optionally wherein R^(E1) and R^(E3) or R^(E2) and R^(E3) or R^(E1) andR^(E2) are joined to form an optionally substituted carbocyclic oroptionally substituted heterocyclic ring;

R^(E4) is a leaving group;

Y is O, S, or NR^(E5), wherein R^(E5) is hydrogen, C₁₋₆ alkyl, or anitrogen protecting group;

a is 1 or 2; and

z is 0, 1, 2, 3, 4, 5, or 6.

Compounds of Formula (I) include a substituted or unsubstitutedcarbocyclic, heterocyclic, heteroaryl, or aryl ring as Ring A. Ring Amay be substituted with one or more substitutents R^(A). In certainembodiments, Ring A is a carbocyclic ring. In certain embodiments, RingA is a monocyclic carbocyclic ring. In certain embodiments, Ring A is abicyclic carbocyclic ring. In certain embodiments, Ring A is a tricycliccarbocyclic ring. In certain embodiments, Ring A is a substitutedcarbocyclic ring. In certain embodiments, Ring A is an unsubstitutedcarbocyclic ring. In certain embodiments, Ring A is a saturatedcarbocyclic ring. In certain embodiments, Ring A is an unsaturatedcarbocyclic ring. In certain embodiments, Ring A is a carbocyclic ringfused with one or more carbocyclic, heterocyclic, aryl, or heteroarylgroups wherein the point of attachment is on the carbocyclic ring.

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is a heterocyclic ring. In certainembodiments, Ring A is a monocyclic heterocyclic ring. In certainembodiments, Ring A is a bicyclic heterocyclic ring. In certainembodiments, Ring A is a tricyclic heterocyclic ring. In certainembodiments, Ring A is a substituted heterocyclic ring. In certainembodiments, Ring A is an unsubstituted heterocyclic ring. In certainembodiments, Ring A is a saturated heterocyclic ring. In certainembodiments, Ring A is an unsaturated heterocyclic ring. In certainembodiments, Ring A is a heterocyclic ring fused with one or morecarbocyclic, heterocyclic, aryl, or heteroaryl groups wherein the pointof attachment is on the heterocyclic ring.

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is an aryl ring. In certain embodiments,Ring A is a monocyclic aryl ring. In certain embodiments, Ring A is abicyclic aryl ring. In certain embodiments, Ring A is a tricyclic arylring. In certain embodiments, Ring A is a substituted aryl ring. Incertain embodiments, Ring A is an unsubstituted aryl ring. In certainembodiments, Ring A is substituted phenyl. In certain embodiments, RingA is unsubstituted phenyl. In certain embodiments, Ring A is an arylring fused with one or more carbocyclic, heterocyclic, aryl, orheteroaryl groups wherein the point of attachment is on the aryl ring.In certain embodiments, Ring A is substituted naphthyl. In certainembodiments, Ring A is unsubstituted naphthyl.

In certain embodiments, Ring A is

In certain embodiments, Ring A is

Ring A of Formula (I) may also be an optionally substituted heteroarylring. In certain embodiments, Ring A is a substituted heteroaryl ring.In certain embodiments, Ring A is an unsubstituted heteroaryl ring. Incertain embodiments, Ring A is a monocyclic heteroaryl ring. In certainembodiments, Ring A is a 5-membered monocyclic heteroaryl ring. Incertain embodiments, Ring A is a 5-membered monocyclic heteroaryl ringwith one heteroatom selected from the group consisting of S, N, and O.In certain embodiments, Ring A is a 5-membered monocyclic heteroarylring with two heteroatoms selected from the group consisting of S, N,and O. In certain embodiments, Ring A is a 5-membered monocyclicheteroaryl ring with three heteroatoms selected from the groupconsisting of S, N, and O. In certain embodiments, Ring A is substitutedpyrrolyl. In certain embodiments, Ring A is unsubstituted pyrrolyl. Incertain embodiments, Ring A is substituted furanyl. In certainembodiments, Ring A is unsubstituted furanyl. In certain embodiments,Ring A is substituted thienyl. In certain embodiments, Ring A isunsubstituted thienyl. In certain embodiments, Ring A is substitutedpyrazolyl. In certain embodiments, Ring A is unsubstituted pyrazolyl. Incertain embodiments, Ring A is substituted imidazolyl. In certainembodiments, Ring A is unsubstituted imidazolyl. In certain embodiments,Ring A is substituted oxazolyl. In certain embodiments, Ring A isunsubstituted oxazolyl. In certain embodiments, Ring A is substitutedisoxazolyl. In certain embodiments, Ring A is unsubstituted isoxazolyl.In certain embodiments, Ring A is substituted thiazolyl. In certainembodiments, Ring A is unsubstituted thiazolyl. In certain embodiments,Ring A is substituted isothiazolyl. In certain embodiments, Ring A isunsubstituted isothiazolyl. In certain embodiments, Ring A issubstituted triazolyl. In certain embodiments, Ring A is unsubstitutedtriazolyl. In certain embodiments, Ring A is substituted oxadiazolyl. Incertain embodiments, Ring A is unsubstituted oxadiazolyl. In certainembodiments, Ring A is substituted thiadiazolyl. In certain embodiments,Ring A is unsubstituted thiadiazolyl. In certain embodiments, Ring A isa 6-membered monocyclic heteroaryl ring. In certain embodiments, Ring Ais a 6-membered monocyclic heteroaryl ring with one heteroatom selectedfrom the group consisting of S, N, and O. In certain embodiments, Ring Ais a 6-membered monocyclic heteroaryl ring with two heteroatoms selectedfrom the group consisting of S, N, and O. In certain embodiments, Ring Ais a 6-membered monocyclic heteroaryl ring with three heteroatomsselected from the group consisting of S, N, and O. In certainembodiments, Ring A is substituted pyridyl. In certain embodiments, RingA is unsubstituted pyridyl. In certain embodiments, Ring A issubstituted pyridazinyl. In certain embodiments, Ring A is unsubstitutedpyridazinyl. In certain embodiments, Ring A is substituted pyrimidinyl.In certain embodiments, Ring A is unsubstituted pyrimidinyl. In certainembodiments, Ring A is substituted pyrazinyl. In certain embodiments,Ring A is unsubstituted pyrazinyl. In certain embodiments, Ring A issubstituted triazinyl. In certain embodiments, Ring A is unsubstitutedtriazinyl. In certain embodiments, Ring A is an optionally substitutedheteroaryl ring fused with one or more optionally substitutedcarbocyclic, optionally substituted heterocyclic, optionally substitutedaryl, or optionally substituted heteroaryl groups wherein the point ofattachment is on any one of the heteroaryl ring, or carbocyclic,heterocyclic, aryl, or heteroaryl groups, as valency permits. In certainembodiments, Ring A is a bicyclic heteroaryl ring. In certainembodiments, Ring A is an optionally substituted heteroaryl ring fusedwith an optionally substituted phenyl ring. In certain embodiments, RingA is substituted indolyl. In certain embodiments, Ring A isunsubstituted indolyl. In certain embodiments, Ring A is substitutedisoindolyl. In certain embodiments, Ring A is unsubstituted isoindolyl.In certain embodiments, Ring A is substituted indazolyl. In certainembodiments, Ring A is unsubstituted indazolyl. In certain embodiments,Ring A is substituted benzothienyl. In certain embodiments, Ring A isunsubstituted benzothienyl. In certain embodiments, Ring A issubstituted isobenzothienyl. In certain embodiments, Ring A isunsubstituted isobenzothienyl. In certain embodiments, Ring A issubstituted benzofuranyl. In certain embodiments, Ring A isunsubstituted benzofuranyl. In certain embodiments, Ring A issubstituted benzoisofuranyl. In certain embodiments, Ring A isunsubstituted benzoisofuranyl. In certain embodiments, Ring A issubstituted benzimidazolyl. In certain embodiments, Ring A isunsubstituted benzimidazolyl. In certain embodiments, Ring A issubstituted benzoxazolyl. In certain embodiments, Ring A isunsubstituted benzoxazolyl. In certain embodiments, Ring A issubstituted benzisoxazolyl. In certain embodiments, Ring A isunsubstituted benzisoxazolyl. In certain embodiments, Ring A issubstituted benzothiazolyl. In certain embodiments, Ring A isunsubstituted benzothiazolyl. In certain embodiments, Ring A issubstituted benzisothiazolyl. In certain embodiments, Ring A isunsubstituted benzisothiazolyl. In certain embodiments, Ring A issubstituted benzotriazolyl. In certain embodiments, Ring A isunsubstituted benzotriazolyl. In certain embodiments, Ring A issubstituted benzoxadiazolyl. In certain embodiments, Ring A isunsubstituted benzoxadiazolyl. In certain embodiments, Ring A issubstituted quinolinyl. In certain embodiments, Ring A is unsubstitutedquinolinyl. In certain embodiments, Ring A is substituted isoquinolinyl.In certain embodiments, Ring A is unsubstituted isoquinolinyl. Incertain embodiments, Ring A is substituted cinnolinyl. In certainembodiments, Ring A is unsubstituted cinnolinyl. In certain embodiments,Ring A is substituted quinoxalinyl. In certain embodiments, Ring A isunsubstituted quinoxalinyl. In certain embodiments, Ring A issubstituted phthalazinyl. In certain embodiments, Ring A isunsubstituted phthalazinyl. In certain embodiments, Ring A issubstituted quinazolinyl. In certain embodiments, Ring A isunsubstituted quinazolinyl. In certain embodiments, Ring A is atricyclic heteroaryl ring.

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, at least one R^(A) is H. In certain embodiments,at least one R^(A) is halogen. In certain embodiments, at least oneR^(A) is F. In certain embodiments, at least one R^(A) is Cl. In certainembodiments, at least one R^(A) is Br. In certain embodiments, at leastone R^(A) is I (iodine). In certain embodiments, at least one R^(A) isacyl. In certain embodiments, at least one R^(A) is acetyl. In certainembodiments, at least one R^(A) is substituted alkyl. In certainembodiments, at least one R^(A) is unsubstituted alkyl. In certainembodiments, at least one R^(A) is C₁₋₆ alkyl. In certain embodiments,at least one R^(A) is methyl. In certain embodiments, at least one R^(A)is ethyl. In certain embodiments, at least one R^(A) is propyl. Incertain embodiments, at least one R^(A) is butyl. In certainembodiments, at least one R^(A) is substituted alkenyl. In certainembodiments, at least one R^(A) is unsubstituted alkenyl. In certainembodiments, at least one R^(A) is substituted alkynyl. In certainembodiments, at least one R^(A) is unsubstituted alkynyl. In certainembodiments, at least one R^(A) is substituted carbocyclyl. In certainembodiments, at least one R^(A) is unsubstituted carbocyclyl. In certainembodiments, at least one R^(A) is substituted heterocyclyl. In certainembodiments, at least one R^(A) is unsubstituted heterocyclyl. Incertain embodiments, at least one R^(A) is substituted aryl. In certainembodiments, at least one R^(A) is unsubstituted aryl. In certainembodiments, at least one R^(A) is substituted phenyl. In certainembodiments, at least one R^(A) is unsubstituted phenyl. In certainembodiments, at least one R^(A) is substituted heteroaryl. In certainembodiments, at least one R^(A) is unsubstituted heteroaryl. In certainembodiments, at least one R^(A) is substituted pyridyl. In certainembodiments, at least one R^(A) is unsubstituted pyridyl. In certainembodiments, at least one R^(A) is —OR^(Al). In certain embodiments, atleast one R^(A) is —N(R^(A1))₂. In certain embodiments, at least oneR^(A) is —SR^(A1).

In certain embodiments, when R^(A) is —OR^(A1), —N(R^(A1), or —SR^(A1),at least one R^(A1) is H. In certain embodiments, at least one R^(A1) isacyl. In certain embodiments, at least one R^(A1) is acetyl. In certainembodiments, at least one R^(A1) is substituted alkyl. In certainembodiments, at least one R^(A1) is unsubstituted alkyl. In certainembodiments, at least one R^(A1) is C₁₋₆ alkyl. In certain embodiments,at least one R^(A1) is methyl. In certain embodiments, at least oneR^(A1) is ethyl. In certain embodiments, at least one R^(A1) is propyl.In certain embodiments, at least one R^(A1) is butyl. In certainembodiments, at least one R^(A1) is substituted alkenyl. In certainembodiments, at least one R^(A1) is unsubstituted alkenyl. In certainembodiments, at least one R^(A1) is substituted alkynyl. In certainembodiments, at least one R^(A1) is unsubstituted alkynyl. In certainembodiments, at least one R^(A1) is substituted carbocyclyl. In certainembodiments, at least one R^(A1) is unsubstituted carbocyclyl. Incertain embodiments, at least one R^(A1) is substituted heterocyclyl. Incertain embodiments, at least one R^(A1) is unsubstituted heterocyclyl.In certain embodiments, at least one R^(A1) is substituted aryl. Incertain embodiments, at least one R^(A1) is unsubstituted aryl. Incertain embodiments, at least one R^(A1) is substituted phenyl. Incertain embodiments, at least one R^(A1) is unsubstituted phenyl. Incertain embodiments, at least one R^(A1) is substituted heteroaryl. Incertain embodiments, at least one R^(A1) is unsubstituted heteroaryl. Incertain embodiments, at least one R^(A1) is substituted pyridyl. Incertain embodiments, at least one R^(A1) is unsubstituted pyridyl. Incertain embodiments, at least one R^(A1) is a nitrogen protecting groupwhen attached to a nitrogen atom. In certain embodiments, at least oneR^(A1) is an oxygen protecting group when attached to an oxygen atom. Incertain embodiments, at least one R^(A1) is a sulfur protecting groupwhen attached to a sulfur atom. In certain embodiments, two R^(A1)groups are joined to form a substituted heterocyclic ring. In certainembodiments, two R^(A1) groups are joined to form an unsubstitutedheterocyclic ring.

Ring A may be unsubstituted or substituted with one or more R^(A). Incertain embodiments, Ring A is unsubstituted, and thus m is 0. Incertain embodiments, m is 1. In certain embodiments, m is 2. In certainembodiments, m is 3. In certain embodiments, m is 4.

Compounds of Formula (I) include a substituted or unsubstitutedheteroaryl ring as Ring B. Ring B may be substituted with onesubstituent R^(B1) or two substituents R^(B1) and R^(B2).

In certain embodiments, Ring B is

In certain embodiments, Ring B is

In certain embodiments, R^(B1) is H. In certain embodiments, R^(B1) ishalogen. In certain embodiments, R^(B1) is F. In certain embodiments,R^(B1) is Cl. In certain embodiments, R^(B1) is Br. In certainembodiments, R^(B1) is I (iodine). In certain embodiments, R^(B1) isacyl. In certain embodiments, R^(B1) is acetyl. In certain embodiments,R^(B1) is substituted alkyl. In certain embodiments, R^(B1) isunsubstituted alkyl. In certain embodiments, R^(B1) is C₁₋₆ alkyl. Incertain embodiments, R^(B1) is methyl. In certain embodiments, R^(B1) isethyl. In certain embodiments, R^(B1) is propyl. In certain embodiments,R^(B1) is butyl. In certain embodiments, R^(B1) is substituted alkenyl.In certain embodiments, R^(B1) is unsubstituted alkenyl. In certainembodiments, R^(B1) is substituted alkynyl. In certain embodiments,R^(B1) is unsubstituted alkynyl. In certain embodiments, R^(B1) issubstituted carbocyclyl. In certain embodiments, R^(B1) is unsubstitutedcarbocyclyl. In certain embodiments, R^(B1) is substituted heterocyclyl.In certain embodiments, R^(B1) is unsubstituted heterocyclyl. In certainembodiments, R^(B1) is substituted aryl. In certain embodiments, R^(B1)is unsubstituted aryl. In certain embodiments, R^(B1) is substitutedphenyl. In certain embodiments, R^(B1) is unsubstituted phenyl. Incertain embodiments, R^(B1) is substituted heteroaryl. In certainembodiments, R^(B1) is unsubstituted heteroaryl. In certain embodiments,R^(B1) is substituted pyridyl. In certain embodiments, R^(B1) isunsubstituted pyridyl. In certain embodiments, R^(B1) is —OR^(B1a). Incertain embodiments, R^(B1) is —N(R^(B1a))₂. In certain embodiments,R^(B1) is —SR^(B1a).

In certain embodiments, at least one R^(B1a) is H. In certainembodiments, at least one R^(B1a) is acyl. In certain embodiments, atleast one R^(B1a) is acetyl. In certain embodiments, at least oneR^(B1a) is substituted alkyl. In certain embodiments, at least oneR^(B1a) is unsubstituted alkyl. In certain embodiments, at least oneR^(B1a) is C₁₋₆ alkyl. In certain embodiments, at least one R^(B1a) ismethyl. In certain embodiments, at least one R^(B1a) is ethyl. Incertain embodiments, at least one R^(B1a) is propyl. In certainembodiments, at least one R^(B1a) is butyl. In certain embodiments, atleast one R^(B1a) is substituted alkenyl. In certain embodiments, atleast one R^(B1a) is unsubstituted alkenyl. In certain embodiments, atleast one R^(B1a) is substituted alkynyl. In certain embodiments, atleast one R^(B1a) is unsubstituted alkynyl. In certain embodiments, atleast one R^(B1a) is substituted carbocyclyl. In certain embodiments, atleast one R^(B1a) is unsubstituted carbocyclyl. In certain embodiments,at least one R^(B1a) is substituted heterocyclyl. In certainembodiments, at least one R^(B1a) is unsubstituted heterocyclyl. Incertain embodiments, at least one R^(B1a) is substituted aryl. Incertain embodiments, at least one R^(B1a) is unsubstituted aryl. Incertain embodiments, at least one R^(B1a) is substituted phenyl. Incertain embodiments, at least one R^(B1a) is unsubstituted phenyl. Incertain embodiments, at least one R^(B1a) is substituted heteroaryl. Incertain embodiments, at least one R^(B1a) is unsubstituted heteroaryl.In certain embodiments, at least one R^(B1a) is substituted pyridyl. Incertain embodiments, at least one R^(B1a) is unsubstituted pyridyl. Incertain embodiments, at least one R^(B1a) is a nitrogen protecting groupwhen attached to a nitrogen atom. In certain embodiments, at least oneR^(B1a) is an oxygen protecting group when attached to an oxygen atom.In certain embodiments, at least one R^(B1a) is a sulfur protectinggroup when attached to a sulfur atom. In certain embodiments, twoR^(B1a) groups are joined to form a substituted heterocyclic ring. Incertain embodiments, two R^(B1a) groups are joined to form anunsubstituted heterocyclic ring.

In certain embodiments, R^(B2) is H. In certain embodiments, R^(B2) ishalogen. In certain embodiments, R^(B2) is F. In certain embodiments,R^(B2) is Cl. In certain embodiments, R^(B2) is Br. In certainembodiments, R^(B2) is I (iodine). In certain embodiments, R^(B2) isacyl. In certain embodiments, R^(B2) is acetyl. In certain embodiments,R^(B2) is substituted alkyl. In certain embodiments, R^(B2) isunsubstituted alkyl. In certain embodiments, R^(B2) is C₁₋₆ alkyl. Incertain embodiments, R^(B2) is methyl. In certain embodiments, R^(B2) isethyl. In certain embodiments, R^(B2) is propyl. In certain embodiments,R^(B2) is butyl. In certain embodiments, R^(B2) is substituted alkenyl.In certain embodiments, R^(B2) is unsubstituted alkenyl. In certainembodiments, R^(B2) is substituted alkynyl. In certain embodiments,R^(B2) is unsubstituted alkynyl. In certain embodiments, R^(B2) issubstituted carbocyclyl. In certain embodiments, R^(B2) is unsubstitutedcarbocyclyl. In certain embodiments, R^(B2) is substituted heterocyclyl.In certain embodiments, R^(B2) is unsubstituted heterocyclyl. In certainembodiments, R^(B2) is substituted aryl. In certain embodiments, R^(B2)is unsubstituted aryl. In certain embodiments, R^(B2) is substitutedphenyl. In certain embodiments, R^(B2) is unsubstituted phenyl. Incertain embodiments, R^(B2) is substituted heteroaryl. In certainembodiments, R^(B2) is unsubstituted heteroaryl. In certain embodiments,R^(B2) is substituted pyridyl. In certain embodiments, R^(B2) isunsubstituted pyridyl. In certain embodiments, R^(B2) is —OR^(B2a). Incertain embodiments, R^(B2) is —N(R^(B2a))₂. In certain embodiments,R^(B2) is —SR^(B2a).

In certain embodiments, at least one R^(B2a) is H. In certainembodiments, at least one R^(B2a) is acyl. In certain embodiments, atleast one R^(B2a) is acetyl. In certain embodiments, at least oneR^(B2a) is substituted alkyl. In certain embodiments, at least oneR^(B2a) is unsubstituted alkyl. In certain embodiments, at least oneR^(B2a) is C₁₋₆ alkyl. In certain embodiments, at least one R^(B2a) ismethyl. In certain embodiments, at least one R^(B2a) is ethyl. Incertain embodiments, at least one R^(B2a) is propyl. In certainembodiments, at least one R^(B2a) is butyl. In certain embodiments, atleast one R^(B2a) is substituted alkenyl. In certain embodiments, atleast one R^(B2a) is unsubstituted alkenyl. In certain embodiments, atleast one R^(B2a) is substituted alkynyl. In certain embodiments, atleast one R^(B2a) is unsubstituted alkynyl. In certain embodiments, atleast one R^(B2a) is substituted carbocyclyl. In certain embodiments, atleast one R^(B2a) is unsubstituted carbocyclyl. In certain embodiments,at least one R^(B2a) is substituted heterocyclyl. In certainembodiments, at least one R^(B2a) is unsubstituted heterocyclyl. Incertain embodiments, at least one R^(B2a) is substituted aryl. Incertain embodiments, at least one R^(B2a) is unsubstituted aryl. Incertain embodiments, at least one R^(B2a) is substituted phenyl. Incertain embodiments, at least one R^(B2a) is unsubstituted phenyl. Incertain embodiments, at least one R^(B2a) is substituted heteroaryl. Incertain embodiments, at least one R^(B2a) is unsubstituted heteroaryl.In certain embodiments, at least one R^(B2a) is substituted pyridyl. Incertain embodiments, at least one R^(B2a) is unsubstituted pyridyl. Incertain embodiments, at least one R^(B2a) is a nitrogen protecting groupwhen attached to a nitrogen atom. In certain embodiments, at least oneR^(B2a) is an oxygen protecting group when attached to an oxygen atom.In certain embodiments, at least one R^(B2a) is a sulfur protectinggroup when attached to a sulfur atom. In certain embodiments, twoR^(B2a) groups are joined to form a substituted heterocyclic ring. Incertain embodiments, two R^(B2a) groups are joined to form anunsubstituted heterocyclic ring.

In certain embodiments, R^(B1) and R^(B2) are joined to form asubstituted carbocyclic ring. In certain embodiments, R^(B1) and R^(B2)are joined to form an unsubstituted carbocyclic ring. In certainembodiments, R^(B1) and R^(B2) are joined to form a substitutedheterocyclic ring. In certain embodiments, R^(B1) and R^(B2) are joinedto form an unsubstituted heterocyclic ring. In certain embodiments,R^(B1) and R^(B2) are joined to form a substituted heteroaryl ring. Incertain embodiments, R^(B1) and R^(B2) are joined to form anunsubstituted heteroaryl ring. In certain embodiments, R^(B1) and R^(B2)are joined to form a substituted pyridyl ring. In certain embodiments,R^(B1) and R^(B2) are joined to form an unsubstituted pyridyl ring. Incertain embodiments, R^(B1) and R^(B2) are joined to form a substitutedaryl ring. In certain embodiments, R^(B1) and R^(B2) are joined to forman unsubstituted aryl ring. In certain embodiments, R^(B1) and R^(B2)are joined to form a substituted phenyl ring. In certain embodiments,R^(B1) and R^(B2) are joined to form an unsubstituted phenyl ring.

In certain embodiments, Ring B is a group selected from the groupconsisting of:

wherein:

R^(B3) is selected from the group consisting of hydrogen, halogen,optionally substituted acyl, optionally substituted alkyl, optionallysubstituted alkenyl, optionally substituted alkynyl, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, optionally substituted heteroaryl, —OR^(B3a,)N(R^(B3a))₂, and —SR^(B3a,) wherein each occurrence of R^(B3a) isindependently selected from the group consisting of hydrogen, acyl,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, a nitrogen protecting group when attached to anitrogen atom, an oxygen protecting group when attached to an oxygenatom, a sulfur protecting group when attached to a sulfur atom, or twoR^(B3a) groups are joined to form an optionally substituted heterocyclicring; and

q is 0, 1, 2, or 3.

In certain embodiments, R^(B3) is H. In certain embodiments, R^(B3) ishalogen. In certain embodiments, R^(B3) is F. In certain embodiments,R^(B3) is Cl. In certain embodiments, R^(B3) is Br. In certainembodiments, R^(B3) is I (iodine). In certain embodiments, R^(B3) isacyl. In certain embodiments, R^(B3) is acetyl. In certain embodiments,R^(B3) is substituted alkyl. In certain embodiments, R^(B3) isunsubstituted alkyl. In certain embodiments, R^(B3) is C₁₋₆ alkyl. Incertain embodiments, R^(B3) is methyl. In certain embodiments, R^(B3) isethyl. In certain embodiments, R^(B3) is propyl. In certain embodiments,R^(B3) is butyl. In certain embodiments, R^(B3) is substituted alkenyl.In certain embodiments, R^(B3) is unsubstituted alkenyl. In certainembodiments, R^(B3) is substituted alkynyl. In certain embodiments,R^(B3) is unsubstituted alkynyl. In certain embodiments, R^(B3) issubstituted carbocyclyl. In certain embodiments, R^(B3) is unsubstitutedcarbocyclyl. In certain embodiments, R^(B3) is substituted heterocyclyl.In certain embodiments, R^(B3) is unsubstituted heterocyclyl. In certainembodiments, R^(B3) is substituted aryl. In certain embodiments, R^(B3)is unsubstituted aryl. In certain embodiments, R^(B3) is substitutedphenyl. In certain embodiments, R^(B3) is unsubstituted phenyl. Incertain embodiments, R^(B3) is substituted heteroaryl. In certainembodiments, R^(B3) is unsubstituted heteroaryl. In certain embodiments,R^(B3) is substituted pyridyl. In certain embodiments, R^(B3) isunsubstituted pyridyl. In certain embodiments, R^(B3) is —OR^(B3a). Incertain embodiments, R^(B3) is N(R^(B3a))₂. In certain embodiments,R^(B3) is —SR^(B3a).

In certain embodiments, at least one R^(B3a) is H. In certainembodiments, at least one R^(B3a) is acyl. In certain embodiments, atleast one R^(B3a) is acetyl. In certain embodiments, at least oneR^(B3a) is substituted alkyl. In certain embodiments, at least oneR^(B3a) is unsubstituted alkyl. In certain embodiments, at least oneR^(B3a) is C₁₋₆ alkyl. In certain embodiments, at least one R^(B3a) ismethyl. In certain embodiments, at least one R^(B3a) is ethyl. Incertain embodiments, at least one R^(B3a) is propyl. In certainembodiments, at least one R^(B3a) is butyl. In certain embodiments, atleast one R^(B3a) is substituted alkenyl. In certain embodiments, atleast one R^(B3a) is unsubstituted alkenyl. In certain embodiments, atleast one R^(B3a) is substituted alkynyl. In certain embodiments, atleast one R^(B3a) is unsubstituted alkynyl. In certain embodiments, atleast one R^(B3a) is substituted carbocyclyl. In certain embodiments, atleast one R^(B3a) is unsubstituted carbocyclyl. In certain embodiments,at least one R^(B3a) is substituted heterocyclyl. In certainembodiments, at least one R^(B3a) is unsubstituted heterocyclyl. Incertain embodiments, at least one R^(B3a) is substituted aryl. Incertain embodiments, at least one R^(B3a) is unsubstituted aryl. Incertain embodiments, at least one R^(B3a) is substituted phenyl. Incertain embodiments, at least one R^(B3a) is unsubstituted phenyl. Incertain embodiments, at least one R^(B3a) is substituted heteroaryl. Incertain embodiments, at least one R^(B3a) is unsubstituted heteroaryl.In certain embodiments, at least one R^(B3a) is substituted pyridyl. Incertain embodiments, at least one R^(B3a) is unsubstituted pyridyl. Incertain embodiments, at least one R^(B3a) is a nitrogen protecting groupwhen attached to a nitrogen atom. In certain embodiments, at least oneR^(B3a) is an oxygen protecting group when attached to an oxygen atom.In certain embodiments, at least one R^(B3a) is a sulfur protectinggroup when attached to a sulfur atom. In certain embodiments, twoR^(B3a) groups are joined to form a substituted heterocyclic ring. Incertain embodiments, two R^(B3a) groups are joined to form anunsubstituted heterocyclic ring.

Ring B may be unsubstituted or substituted with one or more R^(B3). Incertain embodiments, Ring B is unsubstituted, and thus q is 0. Incertain embodiments, q is 1. In certain embodiments, q is 2. In certainembodiments, q is 3.

L₁ is a divalent linker moiety. L₁ may contain 0-4 carbon or heteroatoms in the backbone of L₁. L₁ may be saturated or unsaturated. L₁ maybe substituted or unsubstituted. In certain embodiments, L₁ is a bonddirectly attaching Ring A to Ring B. In certain embodiments, L₁ is asingle bond. In certain embodiments, L₁ is a double bond. In certainembodiments, L₁ is —O—. In certain embodiments, L₁ is —S—. In certainembodiments, L₁ is —NR^(L1b). In certain embodiments, L₁ is —NH—. Incertain embodiments, L₁ is —NR^(L1b)C(═O)—. In certain embodiments, L₁is NHC(═O). In certain embodiments, L₁ is —C(═O)NR^(L1b). In certainembodiments, L₁ is —C(═O)NH—. In certain embodiments, L₁ is —SC(═O)—. Incertain embodiments, L₁ is —C(═O)S—. In certain embodiments, L₁ is—OC(═O)—. In certain embodiments, L₁ is —C(═O)O—. In certainembodiments, L₁ is —NR^(L1b)C(═S)—. In certain embodiments, L₁ is—NHC(═S)—. In certain embodiments, L₁ is —C(═S)NR^(L1b)—. In certainembodiments, L₁ is —C(═S)NH—. In certain embodiments, L₁ istrans-CH═CH—. In certain embodiments, L₁ is cis-CH═CH—. In certainembodiments, L₁ is —S(═O)₂O—. In certain embodiments, L₁ is —OS(═O)₂—.In certain embodiments, L₁ is —S(═O)₂NR^(L1b)—. In certain embodiments,L₁ is —S(═O)₂NH—. In certain embodiments, L₁ is —NR^(L1b)S(═O)₂—. Incertain embodiments, L₁ is —NHS(═O)₂—. In certain embodiments, L₁ is anunsubstituted C₁₋₄ hydrocarbon chain. In certain embodiments, L₁ is asubstituted C₁₋₄ hydrocarbon chain. In certain embodiments, L₁ is asubstituted or unsubstituted C₁₋₄ hydrocarbon chain, wherein onemethylene unit of the hydrocarbon chain is replaced with ═C(R^(L1a))—,—O—, —S—, —NR^(L1b)—, —NR^(L1b)C(═O)—, —C(═O)NR^(L1b)—, —SC(═O),—C(═O)S—, —OC(═O), —C(═O)O—, —NR^(L1b)C(═S)—, —C(═S)NR^(L1b)—,trans-CH═CH—, cis-CH═CH—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(L1b)—, or—NR^(L1b)S(═O)₂—. In certain embodiments, L₁ is —OCH₂—. In certainembodiments, L₁ is —NCH₂—. In certain embodiments, L₁ is —CH₂—.

In certain embodiments, with respect to Formula (I),

between L₁ and Ring A is a single bond. In certain embodiments, withrespect to Formula (I),

is a double bond.

X is a divalent linker moiety. X may be an optionally substituted C₁₋₄hydrocarbon chain, optionally wherein one or more carbon units of thehydrocarbon chain is replaced with —O—, —S—, or —NR^(X)—. In certainembodiments, X is a C₁ hydrocarbon chain, optionally wherein the carbonunit of the hydrocarbon chain is replaced with —O—, —S—, or —NR^(X)—. Incertain embodiments, X is —O—. In certain embodiments, X is —S—. Incertain embodiments, X is —NR^(X)—. In certain embodiments, X is —NH—.In certain embodiments, X is —C(R^(X))₂—. In certain embodiments, X is—CH₂—. In certain embodiments, when X is —NR^(X)— or —C(R^(X))₂—, R^(X)is H. In certain embodiments, R^(X) is substituted alkyl. In certainembodiments, R^(X) is unsubstituted alkyl. In certain embodiments, R^(X)is C₁₋₆ alkyl. In certain embodiments, R^(X) is methyl. In certainembodiments, R^(X) is ethyl. In certain embodiments, R^(X) is propyl. Incertain embodiments, R^(X) is butyl. In certain embodiments, when X is—NR^(X)—, R^(X) is a nitrogen protecting group. In certain embodiments,R^(X) is BOC. In certain embodiments, R^(X) is Cbz. In certainembodiments, R^(X) is Fmoc. In certain embodiments, R^(X) is Bn. Incertain embodiments, X is a C₂ hydrocarbon chain, optionally wherein oneor two carbon units of the hydrocarbon chain is replaced with —O—, —S—,or —NR^(X)—. In certain embodiments, X is a C₃ hydrocarbon chain,optionally wherein one or more carbon units of the hydrocarbon chain isreplaced with —O—, —S—, or —NR^(X)—. In certain embodiments, X is a C₄hydrocarbon chain, optionally wherein one or more carbon units of thehydrocarbon chain is replaced with —O—, —S—, or —NR^(X)—.

In compounds of Formula (I), L₂ is a divalent linker moiety. L₂ maycontain 0-4 carbon or hetero atoms in the backbone of L₂. L₂ may besaturated or unsaturated. L₂ may be substituted or unsubstituted. L₂ maybe branched or unbranched. In certain embodiments, L₂ is a bond. Incertain embodiments, L₂ is —O—. In certain embodiments, L₂ is —S—. Incertain embodiments, L₂ is —NR^(L2a)—. In certain embodiments, L₂ is—NH—. In certain embodiments, L₂ is —NR^(L2a)C(═O)—. In certainembodiments, L₂ is —NHC(═O)—. In certain embodiments, L₂ isC(═O)NR^(L2a)—. In certain embodiments, L₂ is —C(═O)NH—. In certainembodiments, L₂ is —SC(═O)—. In certain embodiments, L₂ is —C(═O)S—. Incertain embodiments, L₂ is —OC(═O)—. In certain embodiments, L₂ is—C(═O)O—. In certain embodiments, L₂ is —NR^(L2a)C(═S)—. In certainembodiments, L₂ is —NHC(═S)—. In certain embodiments, L₂ is—C(═S)NR^(L2a)—. In certain embodiments, L₂ is —C(═S)NH—. In certainembodiments, L₂ is trans-CR^(L2b)═CR^(L2b)—. In certain embodiments, L₂is trans-CH═CH—. In certain embodiments, L₂ is cis-CR^(L2b)═CR^(L2b)—.In certain embodiments, L₂ is cis-CH═CH—. In certain embodiments, L₂ is—C≡C—. In certain embodiments, L₂ is —OC(R^(L2b))₂—. In certainembodiments, L₂ is —OCH₂—. In certain embodiments, L₂ is —C(R^(L2b))₂O—.In certain embodiments, L₂ is —CH₂O—. In certain embodiments, L₂ is—NR^(L2a)C(R^(L2b))²—. In certain embodiments, L₂ is —NR^(L2a)CH₂—. Incertain embodiments, L₂ is —NHCH₂—. In certain embodiments, L₂ is—C(R^(L2b))²NR^(L2a)—. In certain embodiments, L₂ is —CH₂NR^(L2a)—. Incertain embodiments, L₂ is —CH₂NH—. In certain embodiments, L₂ is—SC(R^(L2b))₂—. In certain embodiments, L₂ is —SCH₂—. In certainembodiments, L₂ is —C(R^(L2b))₂S—. In certain embodiments, L₂ is —CH₂S—.In certain embodiments, L₂ is —S(═O)₂O—. In certain embodiments, L₂ is—OS(═O)₂—. In certain embodiments, L₂ is —S(═O)₂NR^(L2a)—. In certainembodiments, L₂ is —S(═O)₂NH—. In certain embodiments, L₂ is—NR^(L2a)S(═O)₂—. In certain embodiments, L₂ is —NHS(═O)₂—. In certainembodiments, L₂ is a substituted C₁₋₄ hydrocarbon chain. In certainembodiments, L₂ is an unsubstituted C₁₋₄ hydrocarbon chain. In certainembodiments, L₂ is a substituted C₂ hydrocarbon chain. In certainembodiments, L₂ is an unsubstituted C₂ hydrocarbon chain. In certainembodiments, L₂ is a substituted C₃ hydrocarbon chain. In certainembodiments, L₂ is an unsubstituted C₃ hydrocarbon chain. In certainembodiments, L₂ is a substituted C₄ hydrocarbon chain. In certainembodiments, L₂ is an unsubstituted C₄ hydrocarbon chain. In certainembodiments, L₂ is an optionally substituted C₁₋₄ hydrocarbon chain,wherein one or more carbon units of the hydrocarbon chain is replacedwith —O—, —S—, —NR^(L2a)—, —NR^(L2a)C(═O)—, —C(═O)NR^(L2a)—, —SC(═O)—,—C(═O)S—, —OC(═O)—, —C(═O)O—, —NR^(L2a)C(═S)NR^(L2a)—,trans-CR^(L2b)═CR^(L2b)—, cis-CR^(L2b)═CR^(L2b)—, —C≡C—, —S(═O)₂O—,—OS(═O)₂—, —S(═O)₂NR^(L2a)—, or —NR^(L2a)S(═O)₂—.

In certain embodiments, R^(L2a) is H. In certain embodiments, R^(L2a) issubstituted alkyl. In certain embodiments, R^(L2a) is unsubstitutedalkyl. In certain embodiments, R^(L2a) is C₁₋₆ alkyl. In certainembodiments, R^(L2a) is methyl. In certain embodiments, R^(L2a) isethyl. In certain embodiments, R^(L2a) is propyl. In certainembodiments, R^(L2a) is butyl. In certain embodiments, R^(L2a) is anitrogen protecting group. In certain embodiments, R^(L2a) is Bn, BOC,Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, or Ts.

In certain embodiments, at least one R^(L2b) is H. In certainembodiments, at least one R^(L2b) is halogen. In certain embodiments, atleast one R^(L2b) is F. In certain embodiments, at least one R^(L2b) isCl. In certain embodiments, at least one R^(L2b) is Br. In certainembodiments, at least one R^(L2b) is I (iodine). In certain embodiments,at least one R^(L2b) is substituted alkyl. In certain embodiments, atleast one R^(L2b) is unsubstituted alkyl. In certain embodiments, atleast one R^(L2b) is C₁₋₆ alkyl. In certain embodiments, at least oneR^(L2b) is methyl. In certain embodiments, at least one R^(L2b) isethyl. In certain embodiments, at least one R^(L2b) is propyl. Incertain embodiments, at least one R^(L2b) is butyl. In certainembodiments, at least one R^(L2b) is substituted alkenyl. In certainembodiments, at least one R^(L2b) is unsubstituted alkenyl. In certainembodiments, at least one R^(L2b) is vinyl. In certain embodiments, atleast one R^(L2b) is substituted alkynyl. In certain embodiments, atleast one R^(L2b) is unsubstituted alkynyl. In certain embodiments, atleast one R^(L2b) is ethynyl. In certain embodiments, at least oneR^(L2b) is substituted carbocyclyl. In certain embodiments, at least oneR^(L2b) is unsubstituted carbocyclyl. In certain embodiments, at leastone R^(L2b) is substituted heterocyclyl. In certain embodiments, atleast one R^(L2b) is unsubstituted heterocyclyl. In certain embodiments,at least one R^(L2b) is substituted aryl. In certain embodiments, atleast one R^(L2b) is unsubstituted aryl. In certain embodiments, atleast one R^(L2b) is substituted phenyl. In certain embodiments, atleast one R^(L2b) is unsubstituted phenyl. In certain embodiments, atleast one R^(L2b) is substituted heteroaryl. In certain embodiments, atleast one R^(L2b) is unsubstituted heteroaryl. In certain embodiments,at least one R^(L2b) is substituted pyridyl. In certain embodiments, atleast one R^(L2b) is unsubstituted pyridyl. In certain embodiments, twoR^(L2b) groups are joined to form a substituted carbocyclic ring. Incertain embodiments, two R^(L2b) groups are joined to form anunsubstituted carbocyclic ring. In certain embodiments, two R^(L2b)groups are joined to form a substituted heterocyclic ring. In certainembodiments, two R^(L2b) groups are joined to form an unsubstitutedheterocyclic ring.

Ring C is a para-phenylene moiety. Ring C may be unsubstituted orsubstituted with one or more substituents R^(C). In certain embodiments,at least one R^(C) is H. In certain embodiments, at least one R^(C) ishalogen. In certain embodiments, at least one R^(C) is F. In certainembodiments, at least one R^(C) is Cl. In certain embodiments, at leastone R^(C) is Br. In certain embodiments, at least one R^(C) is I(iodine). In certain embodiments, at least one R^(C) is acyl. In certainembodiments, at least one R^(C) is acetyl. In certain embodiments, atleast one R^(C) is substituted alkyl. In certain embodiments, at leastone R^(C) is unsubstituted alkyl. In certain embodiments, at least oneR^(C) is C₁₋₆ alkyl. In certain embodiments, at least one R^(C) ismethyl. In certain embodiments, at least one R^(C) is ethyl. In certainembodiments, at least one R^(C) is propyl. In certain embodiments, atleast one R^(C) is butyl. In certain embodiments, at least one R^(C) issubstituted alkenyl. In certain embodiments, at least one R^(C) isunsubstituted alkenyl. In certain embodiments, at least one R^(C) issubstituted alkynyl. In certain embodiments, at least one R^(C) isunsubstituted alkynyl. In certain embodiments, at least one R^(C) issubstituted carbocyclyl. In certain embodiments, at least one R^(C) isunsubstituted carbocyclyl. In certain embodiments, at least one R^(C) issubstituted heterocyclyl. In certain embodiments, at least one R^(C) isunsubstituted heterocyclyl. In certain embodiments, at least one R^(C)is substituted aryl. In certain embodiments, at least one R^(C) isunsubstituted aryl. In certain embodiments, at least one R^(C) issubstituted phenyl. In certain embodiments, at least one R^(C) isunsubstituted phenyl. In certain embodiments, at least one R^(C) issubstituted heteroaryl. In certain embodiments, at least one R^(C) isunsubstituted heteroaryl. In certain embodiments, at least one R^(C) issubstituted pyridyl. In certain embodiments, at least one R^(C) isunsubstituted pyridyl. In certain embodiments, at least one R^(C) is—OR^(C1). In certain embodiments, at least one R^(C) is —N(R^(C1))₂. Incertain embodiments, at least one R^(C) is —SR^(C1).

In certain embodiments, when R^(C) is —OR^(C1), —NR(R^(C1))₂, or—SR^(C1), at least one R^(C1) is H. In certain embodiments, at least oneR^(C1) is acyl. In certain embodiments, at least one R^(C1) is acetyl.In certain embodiments, at least one R^(C1) is substituted alkyl. Incertain embodiments, at least one R^(C1) is unsubstituted alkyl. Incertain embodiments, at least one R^(C1) is C₁₋₆ alkyl. In certainembodiments, at least one R^(C1) is methyl. In certain embodiments, atleast one R^(C1) is ethyl. In certain embodiments, at least one R^(C1)is propyl. In certain embodiments, at least one R^(C1) is butyl. Incertain embodiments, at least one R^(C1) is substituted alkenyl. Incertain embodiments, at least one R^(C1) is unsubstituted alkenyl. Incertain embodiments, at least one R^(C1) is substituted alkynyl. Incertain embodiments, at least one R^(C1) is unsubstituted alkynyl. Incertain embodiments, at least one R^(C1) is substituted carbocyclyl. Incertain embodiments, at least one R^(C1) is unsubstituted carbocyclyl.In certain embodiments, at least one R^(C1) is substituted heterocyclyl.In certain embodiments, at least one R^(C1) is unsubstitutedheterocyclyl. In certain embodiments, at least one R^(C1) is substitutedaryl. In certain embodiments, at least one R^(C1) is unsubstituted aryl.In certain embodiments, at least one R^(C1) is substituted phenyl. Incertain embodiments, at least one R^(C1) is unsubstituted phenyl. Incertain embodiments, at least one R^(C1) is substituted heteroaryl. Incertain embodiments, at least one R^(C1) is unsubstituted heteroaryl. Incertain embodiments, at least one R^(C1) is substituted pyridyl. Incertain embodiments, at least one R^(C1) is unsubstituted pyridyl. Incertain embodiments, at least one R^(C1) is a nitrogen protecting groupwhen attached to a nitrogen atom. In certain embodiments, at least oneR^(C1) is an oxygen protecting group when attached to an oxygen atom. Incertain embodiments, at least one R^(C1) is a sulfur protecting groupwhen attached to a sulfur atom. In certain embodiments, two R^(C1)groups are joined to form a substituted heterocyclic ring. In certainembodiments, two R^(C1) groups are joined to form an unsubstitutedheterocyclic ring.

Ring C may be unsubstituted or substituted with one or more R^(C). Incertain embodiments, Ring C is unsubstituted, and thus n is 0. Incertain embodiments, n is 1. In certain embodiments, n is 2. In certainembodiments, n is 3. In certain embodiments, n is 4.

In certain embodiments, R^(C) is substituted alkyl; and n is 1. Incertain embodiments, R^(C) is unsubstituted alkyl; and n is 1.

Ring D is a meta-phenylene moiety. Ring D may be unsubstituted orsubstituted with one or more substituents R^(D). In certain embodiments,at least one R^(D) is H. In certain embodiments, at least one R^(D) ishalogen. In certain embodiments, at least one R^(D) is F. In certainembodiments, at least one R^(D) is Cl. In certain embodiments, at leastone R^(D) is Br. In certain embodiments, at least one R^(D) is I(iodine). In certain embodiments, at least one R^(D) is acyl. In certainembodiments, at least one R^(D) is acetyl. In certain embodiments, atleast one R^(D) is substituted alkyl. In certain embodiments, at leastone R^(D) is unsubstituted alkyl. In certain embodiments, at least oneR^(D) is C₁₋₆ alkyl. In certain embodiments, at least one R^(D) ismethyl. In certain embodiments, at least one R^(D) is ethyl. In certainembodiments, at least one R^(D) is propyl. In certain embodiments, atleast one R^(D) is butyl. In certain embodiments, at least one R^(D) issubstituted alkenyl. In certain embodiments, at least one R^(D) isunsubstituted alkenyl. In certain embodiments, at least one R^(D) issubstituted alkynyl. In certain embodiments, at least one R^(D) isunsubstituted alkynyl. In certain embodiments, at least one R^(D) issubstituted carbocyclyl. In certain embodiments, at least one R^(D) isunsubstituted carbocyclyl. In certain embodiments, at least one R^(D) issubstituted heterocyclyl. In certain embodiments, at least one R^(D) isunsubstituted heterocyclyl. In certain embodiments, at least one R^(D)is substituted aryl. In certain embodiments, at least one R^(D) isunsubstituted aryl. In certain embodiments, at least one R^(D) issubstituted phenyl. In certain embodiments, at least one R^(D) isunsubstituted phenyl. In certain embodiments, at least one R^(D) issubstituted heteroaryl. In certain embodiments, at least one R^(D) isunsubstituted heteroaryl. In certain embodiments, at least one R^(D) issubstituted pyridyl. In certain embodiments, at least one R^(D) isunsubstituted pyridyl. In certain embodiments, at least one R^(D) is—OR^(D1). In certain embodiments, at least one R^(D) is —N(R^(D1))₂. Incertain embodiments, at least one R^(D) is —SR^(D1).

In certain embodiments, at least one R^(D1) is H. In certainembodiments, at least one R^(D1) is acyl. In certain embodiments, atleast one R^(D1) is acetyl. In certain embodiments, at least one R^(D1)is substituted alkyl. In certain embodiments, at least one R^(D1) isunsubstituted alkyl. In certain embodiments, at least one R^(D1) is C₁₋₆alkyl. In certain embodiments, at least one R^(D1) is methyl. In certainembodiments, at least one R^(D1) is ethyl. In certain embodiments, atleast one R^(D1) is propyl. In certain embodiments, at least one R^(D1)is butyl. In certain embodiments, at least one R^(D1) is substitutedalkenyl. In certain embodiments, at least one R^(D1) is unsubstitutedalkenyl. In certain embodiments, at least one R^(D1) is substitutedalkynyl. In certain embodiments, at least one R^(D1) is unsubstitutedalkynyl. In certain embodiments, at least one R^(D1) is substitutedcarbocyclyl. In certain embodiments, at least one R^(D1) isunsubstituted carbocyclyl. In certain embodiments, at least one R^(D1)is substituted heterocyclyl. In certain embodiments, at least one R^(D1)is unsubstituted heterocyclyl. In certain embodiments, at least oneR^(D1) is substituted aryl. In certain embodiments, at least one R^(D1)is unsubstituted aryl. In certain embodiments, at least one R^(D1) issubstituted phenyl. In certain embodiments, at least one R^(D1) isunsubstituted phenyl. In certain embodiments, at least one R^(D1) issubstituted heteroaryl. In certain embodiments, at least one R^(D1) isunsubstituted heteroaryl. In certain embodiments, at least one R^(D1) issubstituted pyridyl. In certain embodiments, at least one R^(D1) isunsubstituted pyridyl. In certain embodiments, at least one R^(D1) is anitrogen protecting group when attached to a nitrogen atom. In certainembodiments, at least one R^(D1) is an oxygen protecting group whenattached to an oxygen atom. In certain embodiments, at least one R^(D1)is a sulfur protecting group when attached to a sulfur atom. In certainembodiments, two R^(D1) groups are joined to form a substitutedheterocyclic ring. In certain embodiments, two R^(D1) groups are joinedto form an unsubstituted heterocyclic ring.

Ring D may be unsubstituted or substituted with one or more R^(D). Incertain embodiments, Ring D is unsubstituted, and thus p is 0. Incertain embodiments, p is 1. In certain embodiments, p is 2. In certainembodiments, p is 3. In certain embodiments, p is 4.

In certain embodiments, R^(D) is substituted alkyl; and p is 1. Incertain embodiments, R^(D) is unsubstituted alkyl; and p is 1.

R^(E) is a substituent on Ring D, meta to L₂. In certain embodiments,R^(E) is:

In certain embodiments, R^(E) is a group selected from the groupconsisting of:

In compounds of Formula (I), L₃ is a divalent linker moiety. L₃ maycontain 0-4 carbon or hetero atoms in the backbone of L₃. L₃ may besaturated or unsaturated. L₃ may be substituted or unsubstituted. L₃ maybe branched or unbranched. In certain embodiments, L₃ is a bond. Incertain embodiments, L₃ is —O—. In certain embodiments, L₃ is —S—. Incertain embodiments, L₃ is —NR^(L3a). In certain embodiments, L₃ is—NH—. In certain embodiments, L₃ is —NR^(L3a)C(═O)—. In certainembodiments, L₃ is —NHC(═O)—. In certain embodiments, L₃ is—C(═O)NR^(L3a)—. In certain embodiments, L₃ is —C(═O)NH—. In certainembodiments, L₃ is —SC(═O)—. In certain embodiments, L₃ is —C(═O)S—. Incertain embodiments, L₃ is —OC(═O)—. In certain embodiments, L₃ is—C(═O)O—. In certain embodiments, L₃ is —NR^(L3a)C(═S)—. In certainembodiments, L₃ is —NHC(═S)—. In certain embodiments, L₃ is—C(═S)NR^(L3a)—. In certain embodiments, L₃ is —C(═S)NH—. In certainembodiments, L₃ is trans-CR^(L3b)═CR^(L3b)—. In certain embodiments, L₃is trans-CH═CH—. In certain embodiments, L₃ is cis-CR^(L3b)═CR^(L3b)—.In certain embodiments, L₃ is cis-CH═CH—. In certain embodiments, L₃ is—C≡C—. In certain embodiments, L₃ is —OC(R^(L3b))₂—. In certainembodiments, L₃ is —OCH₂—. In certain embodiments, L₃ is —C(R^(L3b))₂O—.In certain embodiments, L₃ is —CH₂O—. In certain embodiments, L₃ is—NR^(L3a)C(R^(L3b))²—. In certain embodiments, L₃ is —NR^(L3a)CH₂—. Incertain embodiments, L₃ is —NHCH₂—. In certain embodiments, L₃ is—C(R^(L3b))₂NR^(L3a)—. In certain embodiments, L₃ is —CH₂NR^(L3a)—. Incertain embodiments, L₃ is —CH₂NH—. In certain embodiments, L₃ is—SC(R^(L3b))₂—. In certain embodiments, L₃ is —SCH₂—. In certainembodiments, L₃ is —C(R^(L3b))₂S—. In certain embodiments, L₃ is —CH₂S—.In certain embodiments, L₃ is —S(═O)₂O—. In certain embodiments, L₃ is—OS(═O)₂—. In certain embodiments, L₃ is —S(═O)₂NR^(L3a)—. In certainembodiments, L₃ is —S(═O)₂NH—. In certain embodiments, L₃ is—NR^(L3a)S(═O)₂—. In certain embodiments, L₃ is —NHS(═O)₂—. In certainembodiments, L₃ is a substituted C₁₋₄ hydrocarbon chain. In certainembodiments, L₃ is an unsubstituted C₁₋₄ hydrocarbon chain. In certainembodiments, L₃ is a substituted C₂ hydrocarbon chain. In certainembodiments, L₃ is an unsubstituted C₂ hydrocarbon chain. In certainembodiments, L₃ is a substituted C₃ hydrocarbon chain. In certainembodiments, L₃ is an unsubstituted C₃ hydrocarbon chain. In certainembodiments, L₃ is a substituted C₄ hydrocarbon chain. In certainembodiments, L₃ is an unsubstituted C₄ hydrocarbon chain. In certainembodiments, L₃ is an optionally substituted C₁₋₄ hydrocarbon chain,wherein one or more carbon units of the hydrocarbon chain is replacedwith —O—, —S—, —NR^(L3a)—, —NR^(L3a)C(═O)—, —C(═O)NR^(L3a)—, —SC(═O)—,—C(═O)S—, —OC(═O)—, —C(═O)O—, —NR^(L3a)C(═S)—, —C(═S)NR^(L3a)—,trans-CR^(L3b)═CR^(L3b)—, cis-CR^(L3b)═CR^(L3b)—, —C≡C—, —S(═O)₂O—,—OS(═O)₂—, —S(═O)₂NR^(L3a)—, or —NR^(L3a)S(═O)₂—.

In certain embodiments, R^(L3a) is H. In certain embodiments, R^(L3a) issubstituted alkyl. In certain embodiments, R^(L3a) is unsubstitutedalkyl. In certain embodiments, R^(L3a) is C₁₋₆ alkyl. In certainembodiments, R^(L3a) is methyl. In certain embodiments, R^(L3a) isethyl. In certain embodiments, R^(L3a) is propyl. In certainembodiments, R^(L3a) is butyl. In certain embodiments, R^(L3a) is anitrogen protecting group. In certain embodiments, R^(L3a) is Bn, BOC,Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, or Ts.

In certain embodiments, at least one R^(L3b) is H. In certainembodiments, at least one R^(L3b) is halogen. In certain embodiments, atleast one R^(L3b) is F. In certain embodiments, at least one R^(L3b) isCl. In certain embodiments, at least one R^(L3b) is Br. In certainembodiments, at least one R^(L3b) is I (iodine). In certain embodiments,at least one R^(L3b) is substituted alkyl. In certain embodiments, atleast one R^(L3b) is unsubstituted alkyl. In certain embodiments, atleast one R^(L3b) is C₁₋₆ alkyl. In certain embodiments, at least oneR^(L3b) is methyl. In certain embodiments, at least one R^(L3b) isethyl. In certain embodiments, at least one R^(L3b) is propyl. Incertain embodiments, at least one R^(L3b) is butyl. In certainembodiments, at least one R^(L3b) is substituted alkenyl. In certainembodiments, at least one R^(L3b) is unsubstituted alkenyl. In certainembodiments, at least one R^(L3b) is vinyl. In certain embodiments, atleast one R^(L3b) is substituted alkynyl. In certain embodiments, atleast one R^(L3b) is unsubstituted alkynyl. In certain embodiments, atleast one R^(L3b) is ethynyl. In certain embodiments, at least oneR^(L3b) is substituted carbocyclyl. In certain embodiments, at least oneR^(L3b) is unsubstituted carbocyclyl. In certain embodiments, at leastone R^(L3b) is substituted heterocyclyl. In certain embodiments, atleast one R^(L3b) is unsubstituted heterocyclyl. In certain embodiments,at least one R^(L3b) is substituted aryl. In certain embodiments, atleast one R^(L3b) is unsubstituted aryl. In certain embodiments, atleast one R^(L3b) is substituted phenyl. In certain embodiments, atleast one R^(L3b) is unsubstituted phenyl. In certain embodiments, atleast one R^(L3b) is substituted heteroaryl. In certain embodiments, atleast one R^(L3b) is unsubstituted heteroaryl. In certain embodiments,at least one R^(L3b) is substituted pyridyl. In certain embodiments, atleast one R^(L3b) is unsubstituted pyridyl. In certain embodiments, twoR^(L3b) groups are joined to form a substituted carbocyclic ring. Incertain embodiments, two R^(L3b) groups are joined to form anunsubstituted carbocyclic ring. In certain embodiments, two R^(L3b)groups are joined to form a substituted heterocyclic ring. In certainembodiments, two R^(L3b) groups are joined to form an unsubstitutedheterocyclic ring.

L₄ is a divalent linker moiety. L₄ may contain 0-4 carbon or heteroatoms in the backbone of L₄. L₄ may be saturated or unsaturated. L₄ maybe substituted or unsubstituted. L₄ may be branched or unbranched. Incertain embodiments, L₄ is a bond. In certain embodiments, L₄ is asubstituted C₁₋₄hydrocarbon chain. In certain embodiments, L₄ is anunsubstituted C₁₋₄ hydrocarbon chain. In certain embodiments, L₄ is—CH₂—. In certain embodiments, L₄ is —CH₂CH₂—. In certain embodiments,L₄ is —CH═CH—. In certain embodiments, L₄ is —(CH₂)₃—. In certainembodiments, L₄ is —(CH₂)₄—.

In certain embodiments, R^(E1) is H. In certain embodiments, R^(E1) ishalogen. In certain embodiments, R^(E1) is F. In certain embodiments,R^(E1) is Cl. In certain embodiments, R^(E1) is Br. In certainembodiments, R^(E1) is I (iodine). In certain embodiments, R^(E1) isacyl. In certain embodiments, R^(E1) is acetyl. In certain embodiments,R^(E1) is substituted alkyl. In certain embodiments, R^(E1) isunsubstituted alkyl. In certain embodiments, R^(E1) is C₁₋₆ alkyl. Incertain embodiments, R^(E1) is methyl. In certain embodiments, R^(E1) isethyl. In certain embodiments, R^(E1) is propyl. In certain embodiments,R^(E1) is butyl. In certain embodiments, R^(E1) is substituted alkenyl.In certain embodiments, R^(E1) is unsubstituted alkenyl. In certainembodiments, R^(E1) is substituted alkynyl. In certain embodiments,R^(E1) is unsubstituted alkynyl. In certain embodiments, R^(E1) issubstituted carbocyclyl. In certain embodiments, R^(E1) is unsubstitutedcarbocyclyl. In certain embodiments, R^(E1) is substituted heterocyclyl.In certain embodiments, R^(E1) is unsubstituted heterocyclyl. In certainembodiments, R^(E1) is substituted aryl. In certain embodiments, R^(E1)is unsubstituted aryl. In certain embodiments, R^(E1) is substitutedphenyl. In certain embodiments, R^(E1) is unsubstituted phenyl. Incertain embodiments, R^(E1) is substituted heteroaryl. In certainembodiments, R^(E1) is unsubstituted heteroaryl. In certain embodiments,R^(E1) is substituted pyridyl. In certain embodiments, R^(E1) isunsubstituted pyridyl. In certain embodiments, R^(E1) is —OR^(E1a). Incertain embodiments, R^(E1) is —N(R^(E1a))₂. In certain embodiments,R^(E1) is —SR^(E1a). In certain embodiments, R^(E1) is —CH₂OR^(E1a). Incertain embodiments, R^(E1) is —CH₂N(R^(E1a))₂. In certain embodiments,R^(E1) is —CH₂SR^(E1a).

In certain embodiments, at least one R^(E1a) is H. In certainembodiments, at least one R^(E1a) is acyl. In certain embodiments, atleast one R^(E1a) is acetyl. In certain embodiments, at least oneR^(E1a) is substituted alkyl. In certain embodiments, at least oneR^(E1a) is unsubstituted alkyl. In certain embodiments, at least oneR^(E1a) is C₁₋₆ alkyl. In certain embodiments, at least one R^(E1a) ismethyl. In certain embodiments, at least one R^(E1a) is ethyl. Incertain embodiments, at least one R^(E1a) is propyl. In certainembodiments, at least one R^(E1a) is butyl. In certain embodiments, atleast one R^(E1a) is substituted alkenyl. In certain embodiments, atleast one R^(E1a) is unsubstituted alkenyl. In certain embodiments, atleast one R^(E1a) is substituted alkynyl. In certain embodiments, atleast one R^(E1a) is unsubstituted alkynyl. In certain embodiments, atleast one R^(E1a) is substituted carbocyclyl. In certain embodiments, atleast one R^(E1a) is unsubstituted carbocyclyl. In certain embodiments,at least one R^(E1a) is substituted heterocyclyl. In certainembodiments, at least one R^(E1a) is unsubstituted heterocyclyl. Incertain embodiments, at least one R^(E1a) is substituted aryl. Incertain embodiments, at least one R^(E1a) is unsubstituted aryl. Incertain embodiments, at least one R^(E1a) is substituted phenyl. Incertain embodiments, at least one R^(E1a) is unsubstituted phenyl. Incertain embodiments, at least one R^(E1a) is substituted heteroaryl. Incertain embodiments, at least one R^(E1a) is unsubstituted heteroaryl.In certain embodiments, at least one R^(E1a) is substituted pyridyl. Incertain embodiments, at least one R^(E1a) is unsubstituted pyridyl. Incertain embodiments, at least one R^(E1a) is a nitrogen protecting groupwhen attached to a nitrogen atom. In certain embodiments, at least oneR^(E1a) is an oxygen protecting group when attached to an oxygen atom.In certain embodiments, at least one R^(E1a) is a sulfur protectinggroup when attached to a sulfur atom. In certain embodiments, twoR^(E1a) groups are joined to form a substituted heterocyclic ring. Incertain embodiments, two R^(E1a) groups are joined to form anunsubstituted heterocyclic ring.

In certain embodiments, R^(E2) is H. In certain embodiments, R^(E2) ishalogen. In certain embodiments, R^(E2) is F. In certain embodiments,R^(E2) is Cl. In certain embodiments, R^(E2) is Br. In certainembodiments, R^(E2) is I (iodine). In certain embodiments, R^(E2) isacyl. In certain embodiments, R^(E2) is acetyl. In certain embodiments,R^(E2) is substituted alkyl. In certain embodiments, R^(E2) isunsubstituted alkyl. In certain embodiments, R^(E2) is C₁₋₆ alkyl. Incertain embodiments, R^(E2) is methyl. In certain embodiments, R^(E2) isethyl. In certain embodiments, R^(E2) is propyl. In certain embodiments,R^(E2) is butyl. In certain embodiments, R^(E2) is substituted alkenyl.In certain embodiments, R^(E2) is unsubstituted alkenyl. In certainembodiments, R^(E2) is substituted alkynyl. In certain embodiments,R^(E2) is unsubstituted alkynyl. In certain embodiments, R^(E2) issubstituted carbocyclyl. In certain embodiments, R^(E2) is unsubstitutedcarbocyclyl. In certain embodiments, R^(E2) is substituted heterocyclyl.In certain embodiments, R^(E2) is unsubstituted heterocyclyl. In certainembodiments, R^(E2) is substituted aryl. In certain embodiments, R^(E2)is unsubstituted aryl. In certain embodiments, R^(E2) is substitutedphenyl. In certain embodiments, R^(E2) is unsubstituted phenyl. Incertain embodiments, R^(E2) is substituted heteroaryl. In certainembodiments, R^(E2) is unsubstituted heteroaryl. In certain embodiments,R^(E2) is substituted pyridyl. In certain embodiments, R^(E2) isunsubstituted pyridyl. In certain embodiments, R^(E2) is —OR^(E2a). Incertain embodiments, R^(E2) is —N(R^(E2a))₂. In certain embodiments,R^(E2) is —SR^(E2a). In certain embodiments, R^(E2) is —CH₂OR^(E2a). Incertain embodiments, R^(E2) is —CH₂N(R^(E2a))₂. In certain embodiments,R^(E2) is —CH₂SR^(E2a).

In certain embodiments, at least one R^(E2a) is H. In certainembodiments, at least one R^(E2a) is acyl. In certain embodiments, atleast one R^(E2a) is acetyl. In certain embodiments, at least oneR^(E2a) is substituted alkyl. In certain embodiments, at least oneR^(E2a) is unsubstituted alkyl. In certain embodiments, at least oneR^(E2a) is C₁₋₆ alkyl. In certain embodiments, at least one R^(E2a) ismethyl. In certain embodiments, at least one R^(E2a) is ethyl. Incertain embodiments, at least one R^(E2a) is propyl. In certainembodiments, at least one R^(E2a) is butyl. In certain embodiments, atleast one R^(E2a) is substituted alkenyl. In certain embodiments, atleast one R^(E2a) is unsubstituted alkenyl. In certain embodiments, atleast one R^(E2a) is substituted alkynyl. In certain embodiments, atleast one R^(E2a) is unsubstituted alkynyl. In certain embodiments, atleast one R^(E2a) is substituted carbocyclyl. In certain embodiments, atleast one R^(E2a) is unsubstituted carbocyclyl. In certain embodiments,at least one R^(E2a) is substituted heterocyclyl. In certainembodiments, at least one R^(E2a) is unsubstituted heterocyclyl. Incertain embodiments, at least one R^(E2a) is substituted aryl. Incertain embodiments, at least one R^(E2a) is unsubstituted aryl. Incertain embodiments, at least one R^(E2a) is substituted phenyl. Incertain embodiments, at least one R^(E2a) is unsubstituted phenyl. Incertain embodiments, at least one R^(E2a) is substituted heteroaryl. Incertain embodiments, at least one R^(E2a) is unsubstituted heteroaryl.In certain embodiments, at least one R^(E2a) is substituted pyridyl. Incertain embodiments, at least one R^(E2a) is unsubstituted pyridyl. Incertain embodiments, at least one R^(E2a) is a nitrogen protecting groupwhen attached to a nitrogen atom. In certain embodiments, at least oneR^(E2a) is an oxygen protecting group when attached to an oxygen atom.In certain embodiments, at least one R^(E2a) is a sulfur protectinggroup when attached to a sulfur atom. In certain embodiments, twoR^(E2a) groups are joined to form a substituted heterocyclic ring. Incertain embodiments, two R^(E2a) groups are joined to form anunsubstituted heterocyclic ring.

In certain embodiments, R^(E3) is H. In certain embodiments, R^(E3) ishalogen. In certain embodiments, R^(E3) is F. In certain embodiments,R^(E3) is Cl. In certain embodiments, R^(E3) is Br. In certainembodiments, R^(E3) is I (iodine). In certain embodiments, R^(E3) isacyl. In certain embodiments, R^(E3) is acetyl. In certain embodiments,R^(E3) is substituted alkyl. In certain embodiments, R^(E3) isunsubstituted alkyl. In certain embodiments, R^(E3) is C₁₋₆ alkyl. Incertain embodiments, R^(E3) is methyl. In certain embodiments, R^(E3) isethyl. In certain embodiments, R^(E3) is propyl. In certain embodiments,R^(E3) is butyl. In certain embodiments, R^(E3) is substituted alkenyl.In certain embodiments, R^(E3) is unsubstituted alkenyl. In certainembodiments, R^(E3) is substituted alkynyl. In certain embodiments,R^(E3) is unsubstituted alkynyl. In certain embodiments, R^(E3) issubstituted carbocyclyl. In certain embodiments, R^(E3) is unsubstitutedcarbocyclyl. In certain embodiments, R^(E3) is substituted heterocyclyl.In certain embodiments, R^(E3) is unsubstituted heterocyclyl. In certainembodiments, R^(E3) is substituted aryl. In certain embodiments, R^(E3)is unsubstituted aryl. In certain embodiments, R^(E3) is substitutedphenyl. In certain embodiments, R^(E3) is unsubstituted phenyl. Incertain embodiments, R^(E3) is substituted heteroaryl. In certainembodiments, R^(E3) is unsubstituted heteroaryl. In certain embodiments,R^(E3) is substituted pyridyl. In certain embodiments, R^(E3) isunsubstituted pyridyl. In certain embodiments, R^(E3) is —OR^(E3a). Incertain embodiments, R^(E3) is —N(R^(E3a))₂. In certain embodiments,R^(E3) is —SR^(E3a). In certain embodiments, R^(E3) is —CH₂OR^(E3a). Incertain embodiments, R^(E3) is —CH₂N(R^(E3a))₂. In certain embodiments,R^(E3) is —CH₂SR^(E3a).

In certain embodiments, at least one R^(E3a) is H. In certainembodiments, at least one R^(E3a) is acyl. In certain embodiments, atleast one R^(E3a) is acetyl. In certain embodiments, at least oneR^(E3a) is substituted alkyl. In certain embodiments, at least oneR^(E3a) is unsubstituted alkyl. In certain embodiments, at least oneR^(E3a) is C₁₋₆ alkyl. In certain embodiments, at least one R^(E3a) ismethyl. In certain embodiments, at least one R^(E3a) is ethyl. Incertain embodiments, at least one R^(E3a) is propyl. In certainembodiments, at least one R^(E3a) is butyl. In certain embodiments, atleast one R^(E3a) is substituted alkenyl. In certain embodiments, atleast one R^(E3a) is unsubstituted alkenyl. In certain embodiments, atleast one R^(E3a) is substituted alkynyl. In certain embodiments, atleast one R^(E3a) is unsubstituted alkynyl. In certain embodiments, atleast one R^(E3a) is substituted carbocyclyl. In certain embodiments, atleast one R^(E3a) is unsubstituted carbocyclyl. In certain embodiments,at least one R^(E3a) is substituted heterocyclyl. In certainembodiments, at least one R^(E3a) is unsubstituted heterocyclyl. Incertain embodiments, at least one R^(E3a) is substituted aryl. Incertain embodiments, at least one R^(E3a) is unsubstituted aryl. Incertain embodiments, at least one R^(E3a) is substituted phenyl. Incertain embodiments, at least one R^(E3a) is unsubstituted phenyl. Incertain embodiments, at least one R^(E3a) is substituted heteroaryl. Incertain embodiments, at least one R^(E3a) is unsubstituted heteroaryl.In certain embodiments, at least one R^(E3a) is substituted pyridyl. Incertain embodiments, at least one R^(E3a) is unsubstituted pyridyl. Incertain embodiments, at least one R^(E3a) is a nitrogen protecting groupwhen attached to a nitrogen atom. In certain embodiments, at least oneR^(E3a) is an oxygen protecting group when attached to an oxygen atom.In certain embodiments, at least one R^(E3a) is a sulfur protectinggroup when attached to a sulfur atom. In certain embodiments, twoR^(E3a) groups are joined to form a substituted heterocyclic ring. Incertain embodiments, two R^(E3a) groups are joined to form anunsubstituted heterocyclic ring.

In compounds of Formula (I), R^(E) may include a substituent R^(E4). Incertain embodiments, R^(E4) is a leaving group. In certain embodiments,R^(E4) is halogen. In certain embodiments, R^(E4) is F. In certainembodiments, R^(E4) is Cl. In certain embodiments, R^(E4) is Br. Incertain embodiments, R^(E4) is I (iodine). In certain embodiments,R^(E4) is —OS(═O)_(w)R^(E4a). In certain embodiments, w is 1. In certainembodiments, w is 2. In certain embodiments, R^(E4) is —OMs. In certainembodiments, R^(E4) is —OTf. In certain embodiments, R^(E4) is —OTs. Incertain embodiments, R^(E4) is —OB s. In certain embodiments, R^(E4) is2-nitrobenzenesulfonyloxy.In certain embodiments, R^(E4) is —OR^(E4a).In certain embodiments, R^(E4) is —OMe. In certain embodiments, R^(E4)is —OCF₃. In certain embodiments, R^(E4) is —OPh. In certainembodiments, R^(E4) is —OC(═O)R^(E4a). In certain embodiments, R^(E4) is—OC(═O)Me. In certain embodiments, R^(E4) is —OC(═O)CF₃. In certainembodiments, R^(E4) is —OC(═O)Ph. In certain embodiments, R^(E4) is—OC(═O)Cl. In certain embodiments, R^(E4) is —OC(═O)OR^(E4a). In certainembodiments, R^(E4) is —OC(═O)OMe. In certain embodiments, R^(E4) is—OC(═O)O(t-Bu).

In certain embodiments, R^(E4a) is substituted alkyl. In certainembodiments, R^(E4a) is unsubstituted alkyl. In certain embodiments,R^(E4a) is substituted alkenyl. In certain embodiments, R^(E4a) isunsubstituted alkenyl. In certain embodiments, R^(E4a) is substitutedalkynyl. In certain embodiments, R^(E4a) is unsubstituted alkynyl. Incertain embodiments, R^(E4a) is substituted carbocyclyl. In certainembodiments, R^(E4a) is unsubstituted carbocyclyl. In certainembodiments, R^(E4a) is substituted heterocyclyl. In certainembodiments, R^(E4a) is unsubstituted heterocyclyl. In certainembodiments, R^(E4a) is substituted aryl. In certain embodiments,R^(E4a) is unsubstituted aryl. In certain embodiments, R^(E4a) issubstituted heteroaryl. In certain embodiments, R^(E4a) is unsubstitutedheteroaryl.

In certain embodiments, Y is O. In certain embodiments, Y is S. Incertain embodiments, Y is NR^(E5). In certain embodiments, Y is NH.

In certain embodiments, R^(E5) is H. In certain embodiments, R^(E5) issubstituted alkyl. In certain embodiments, R^(E5) is unsubstitutedalkyl. In certain embodiments, R^(E5) is C₁₋₆ alkyl. In certainembodiments, R^(E5) is methyl. In certain embodiments, R^(E5) is ethyl.In certain embodiments, R^(E5) is propyl. In certain embodiments, R^(E5)is butyl. In certain embodiments, R^(E5) is a nitrogen protecting group.In certain embodiments, R^(E5) is BOC. In certain embodiments, R^(E5) isCbz. In certain embodiments, R^(E5) is Fmoc. In certain embodiments,R^(E5) is Bn.

In certain embodiments, a is 1. In certain embodiments, a is 2.

In certain embodiments, z is 0. In certain embodiments, z is 1. Incertain embodiments, z is 2. In certain embodiments, z is 3. In certainembodiments, z is 4. In certain embodiments, z is 5. In certainembodiments, z is 6.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compounds of the present invention are thecompounds described herein, and pharmaceutically acceptable salts,solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers,isotopically labeled derivatives, or prodrugs thereof. In certainembodiments, the compounds of the present invention are the compounds ofFormula (I), and pharmaceutically acceptable salts, solvates, hydrates,polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeledderivatives, or prodrugs thereof. In certain embodiments, the compoundsof the present invention are JNK-IN-5, JNK-IN-6, JNK-IN-7, JNK-IN-8,JNK-IN-9, JNK-IN-10, JNK-IN-11, JNK-IN-12, THZ-2-117-1, THZ-2-118-1,THZ-2-140-2, THZ-2-142-1, THZ-2-143-1, THZ-2-144-1, THZ-2-145-1,THZ-2-147-1, THZ-2-148-1, THZ-3-06-1, THZ-3-07-1, THZ-3-11-1,THZ-3-30-1, THZ-3-39-1, and THZ-3-46-1, and pharmaceutically acceptablesalts, solvates, hydrates, polymorphs, co-crystals, tautomers,stereoisomers, isotopically labeled derivatives, or prodrugs thereof.

In certain embodiments, the compound of the present invention is of theformula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof. The compounds THZ-2-071-1, ZG-9, ZG-10, ZG-6, andTHZ-2-102-1 may not have significant activity against JNK; however,these compounds may be useful in inhibiting other kinases.

The compounds of the invention bear multiple binding motifs to JNK. RingA of the inventive compounds may be accommodated inside a hydrophobicpocket in the ATP-binding site of JNK. Functionalities on Ring A maybind to residues of JNK, such as to the “gatekeeper” methionine residue.Ring B of the compounds of the invention may bind to JNK kinase hingeresidues, such as Leu148 and Met149. Functional groups of R^(E) may forma hydrogen bond with JNK's Asn152 residue. This hydrogen bond may beimportant for positioning Ring D and orienting the Michael acceptormoiety proximal to Cys154 to facilitate covalent bond formation. Incertain embodiments, the compounds of the invention non-covalently bindto JNK. In other embodiments, the compounds of the invention covalentlyattach to JNK. In certain embodiments, the covalent attachment of thecompounds of the invention to JNK is irreversible. In other embodiments,the covalent attachment is reversible.

Pharmaceutical Compositions, Kits, and Administration

The present invention provides pharmaceutical compositions comprising acompound of the present invention, e.g., a compound of Formula (I), andpharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,and prodrugs thereof, as described herein, and optionally apharmaceutically acceptable excipient. In certain embodiments, thecompound of the present invention, or a pharmaceutically acceptable saltthereof, is provided in an effective amount in the pharmaceuticalcomposition. In certain embodiments, the effective amount is atherapeutically effective amount. In certain embodiments, the effectiveamount is a prophylactically effective amount.

Pharmaceutical compositions described herein can be prepared by anymethod known in the art of pharmacology. In general, such preparatorymethods include the steps of bringing the compound of the presentinvention (the “active ingredient”) into association with a carrierand/or one or more other accessory ingredients, and then, if necessaryand/or desirable, shaping and/or packaging the product into a desiredsingle- or multi-dose unit.

Pharmaceutical compositions can be prepared, packaged, and/or sold inbulk, as a single unit dose, and/or as a plurality of single unit doses.As used herein, a “unit dose” is a discrete amount of the pharmaceuticalcomposition comprising a predetermined amount of the active ingredient.The amount of the active ingredient is generally equal to the dosage ofthe active ingredient which would be administered to a subject and/or aconvenient fraction of such a dosage such as, for example, one-half orone-third of such a dosage.

Relative amounts of the active ingredient, the pharmaceuticallyacceptable excipient, and/or any additional ingredients in apharmaceutical composition of the invention will vary, depending uponthe identity, size, and/or condition of the subject treated and furtherdepending upon the route by which the composition is to be administered.By way of example, the composition may comprise between 0.1% and 100%(w/w) active ingredient.

Pharmaceutically acceptable excipients used in the manufacture ofprovided pharmaceutical compositions include inert diluents, dispersingand/or granulating agents, surface active agents and/or emulsifiers,disintegrating agents, binding agents, preservatives, buffering agents,lubricating agents, and/or oils. Excipients such as cocoa butter andsuppository waxes, coloring agents, coating agents, sweetening,flavoring, and perfuming agents may also be present in the composition.

Exemplary diluents include calcium carbonate, sodium carbonate, calciumphosphate, dicalcium phosphate, calcium sulfate, calcium hydrogenphosphate, sodium phosphate lactose, sucrose, cellulose,microcrystalline cellulose, kaolin, mannitol, sorbitol, inositol, sodiumchloride, dry starch, cornstarch, powdered sugar, and mixtures thereof.

Exemplary granulating and/or dispersing agents include potato starch,corn starch, tapioca starch, sodium starch glycolate, clays, alginicacid, guar gum, citrus pulp, agar, bentonite, cellulose, and woodproducts, natural sponge, cation-exchange resins, calcium carbonate,silicates, sodium carbonate, cross-linked poly(vinyl-pyrrolidone)(crospovidone), sodium carboxymethyl starch (sodium starch glycolate),carboxymethyl cellulose, cross-linked sodium carboxymethyl cellulose(croscarmellose), methylcellulose, pregelatinized starch (starch 1500),microcrystalline starch, water insoluble starch, calcium carboxymethylcellulose, magnesium aluminum silicate (Veegum), sodium lauryl sulfate,quaternary ammonium compounds, and mixtures thereof.

Exemplary surface active agents and/or emulsifiers include naturalemulsifiers (e.g. acacia, agar, alginic acid, sodium alginate,tragacanth, chondrux, cholesterol, xanthan, pectin, gelatin, egg yolk,casein, wool fat, cholesterol, wax, and lecithin), colloidal clays (e.g.bentonite (aluminum silicate) and Veegum (magnesium aluminum silicate)),long chain amino acid derivatives, high molecular weight alcohols (e.g.stearyl alcohol, cetyl alcohol, oleyl alcohol, triacetin monostearate,ethylene glycol distearate, glyceryl monostearate, and propylene glycolmonostearate, polyvinyl alcohol), carbomers (e.g. carboxy polymethylene,polyacrylic acid, acrylic acid polymer, and carboxyvinyl polymer),carrageenan, cellulosic derivatives (e.g. carboxymethylcellulose sodium,powdered cellulose, hydroxymethyl cellulose, hydroxypropyl cellulose,hydroxypropyl methylcellulose, methylcellulose), sorbitan fatty acidesters (e.g. polyoxyethylene sorbitan monolaurate (Tween 20),polyoxyethylene sorbitan (Tween 60), polyoxyethylene sorbitan monooleate(Tween 80), sorbitan monopalmitate (Span 40), sorbitan monostearate(Span 60), sorbitan tristearate (Span 65), glyceryl monooleate, sorbitanmonooleate (Span 80)), polyoxyethylene esters (e.g. polyoxyethylenemonostearate (Myrj 45), polyoxyethylene hydrogenated castor oil,polyethoxylated castor oil, polyoxymethylene stearate, and Solutol),sucrose fatty acid esters, polyethylene glycol fatty acid esters (e.g.Cremophor™) polyoxyethylene ethers, (e.g. polyoxyethylene lauryl ether(Brij 30)), poly(vinyl-pyrrolidone), diethylene glycol monolaurate,triethanolamine oleate, sodium oleate, potassium oleate, ethyl oleate,oleic acid, ethyl laurate, sodium lauryl sulfate, Pluronic F 68,Poloxamer 188, cetrimonium bromide, cetylpyridinium chloride,benzalkonium chloride, docusate sodium, and/or mixtures thereof.

Exemplary binding agents include starch (e.g. cornstarch and starchpaste), gelatin, sugars (e.g. sucrose, glucose, dextrose, dextrin,molasses, lactose, lactitol, mannitol, etc.), natural and synthetic gums(e.g. acacia, sodium alginate, extract of Irish moss, panwar gum, ghattigum, mucilage of isapol husks, carboxymethylcellulose, methylcellulose,ethylcellulose, hydroxyethylcellulose, hydroxypropyl cellulose,hydroxypropyl methylcellulose, microcrystalline cellulose, celluloseacetate, poly(vinyl-pyrrolidone), magnesium aluminum silicate (Veegum),and larch arabogalactan), alginates, polyethylene oxide, polyethyleneglycol, inorganic calcium salts, silicic acid, polymethacrylates, waxes,water, alcohol, and/or mixtures thereof.

Exemplary preservatives include antioxidants, chelating agents,antimicrobial preservatives, antifungal preservatives, alcoholpreservatives, acidic preservatives, and other preservatives.

Exemplary antioxidants include alpha tocopherol, ascorbic acid, acorbylpalmitate, butylated hydroxyanisole, butylated hydroxytoluene,monothioglycerol, potassium metabisulfite, propionic acid, propylgallate, sodium ascorbate, sodium bisulfite, sodium metabisulfite, andsodium sulfite.

Exemplary chelating agents include ethylenediaminetetraacetic acid(EDTA) and salts and hydrates thereof (e.g., sodium edetate, disodiumedetate, trisodium edetate, calcium disodium edetate, dipotassiumedetate, and the like), citric acid and salts and hydrates thereof(e.g., citric acid monohydrate), fumaric acid and salts and hydratesthereof, malic acid and salts and hydrates thereof, phosphoric acid andsalts and hydrates thereof, and tartaric acid and salts and hydratesthereof. Exemplary antimicrobial preservatives include benzalkoniumchloride, benzethonium chloride, benzyl alcohol, bronopol, cetrimide,cetylpyridinium chloride, chlorhexidine, chlorobutanol, chlorocresol,chloroxylenol, cresol, ethyl alcohol, glycerin, hexetidine, imidurea,phenol, phenoxyethanol, phenylethyl alcohol, phenylmercuric nitrate,propylene glycol, and thimerosal.

Exemplary antifungal preservatives include butyl paraben, methylparaben, ethyl paraben, propyl paraben, benzoic acid, hydroxybenzoicacid, potassium benzoate, potassium sorbate, sodium benzoate, sodiumpropionate, and sorbic acid.

Exemplary alcohol preservatives include ethanol, polyethylene glycol,phenol, phenolic compounds, bisphenol, chlorobutanol, hydroxybenzoate,and phenylethyl alcohol.

Exemplary acidic preservatives include vitamin A, vitamin C, vitamin E,beta-carotene, citric acid, acetic acid, dehydroacetic acid, ascorbicacid, sorbic acid, and phytic acid.

Other preservatives include tocopherol, tocopherol acetate, deteroximemesylate, cetrimide, butylated hydroxyanisol (BHA), butylatedhydroxytoluened (BHT), ethylenediamine, sodium lauryl sulfate (SLS),sodium lauryl ether sulfate (SLES), sodium bisulfite, sodiummetabisulfite, potassium sulfite, potassium metabisulfite, Glydant Plus,Phenonip, methylparaben, Germall 115, Germaben II, Neolone, Kathon, andEuxyl. In certain embodiments, the preservative is an anti-oxidant. Inother embodiments, the preservative is a chelating agent.

Exemplary buffering agents include citrate buffer solutions, acetatebuffer solutions, phosphate buffer solutions, ammonium chloride, calciumcarbonate, calcium chloride, calcium citrate, calcium glubionate,calcium gluceptate, calcium gluconate, D-gluconic acid, calciumglycerophosphate, calcium lactate, propanoic acid, calcium levulinate,pentanoic acid, dibasic calcium phosphate, phosphoric acid, tribasiccalcium phosphate, calcium hydroxide phosphate, potassium acetate,potassium chloride, potassium gluconate, potassium mixtures, dibasicpotassium phosphate, monobasic potassium phosphate, potassium phosphatemixtures, sodium acetate, sodium bicarbonate, sodium chloride, sodiumcitrate, sodium lactate, dibasic sodium phosphate, monobasic sodiumphosphate, sodium phosphate mixtures, tromethamine, magnesium hydroxide,aluminum hydroxide, alginic acid, pyrogen-free water, isotonic saline,Ringer's solution, ethyl alcohol, and mixtures thereof.

Exemplary lubricating agents include magnesium stearate, calciumstearate, stearic acid, silica, talc, malt, glyceryl behanate,hydrogenated vegetable oils, polyethylene glycol, sodium benzoate,sodium acetate, sodium chloride, leucine, magnesium lauryl sulfate,sodium lauryl sulfate, and mixtures thereof.

Exemplary natural oils include almond, apricot kernel, avocado, babassu,bergamot, black current seed, borage, cade, camomile, canola, caraway,carnauba, castor, cinnamon, cocoa butter, coconut, cod liver, coffee,corn, cotton seed, emu, eucalyptus, evening primrose, fish, flaxseed,geraniol, gourd, grape seed, hazel nut, hyssop, isopropyl myristate,jojoba, kukui nut, lavandin, lavender, lemon, litsea cubeba, macademianut, mallow, mango seed, meadowfoam seed, mink, nutmeg, olive, orange,orange roughy, palm, palm kernel, peach kernel, peanut, poppy seed,pumpkin seed, rapeseed, rice bran, rosemary, safflower, sandalwood,sasquana, savoury, sea buckthorn, sesame, shea butter, silicone,soybean, sunflower, tea tree, thistle, tsubaki, vetiver, walnut, andwheat germ oils. Exemplary synthetic oils include, but are not limitedto, butyl stearate, caprylic triglyceride, capric triglyceride,cyclomethicone, diethyl sebacate, dimethicone 360, isopropyl myristate,mineral oil, octyldodecanol, oleyl alcohol, silicone oil, and mixturesthereof.

Liquid dosage forms for oral and parenteral administration includepharmaceutically acceptable emulsions, microemulsions, solutions,suspensions, syrups and elixirs. In addition to the active ingredients,the liquid dosage forms may comprise inert diluents commonly used in theart such as, for example, water or other solvents, solubilizing agentsand emulsifiers such as ethyl alcohol, isopropyl alcohol, ethylcarbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propyleneglycol, 1,3-butylene glycol, dimethylformamide, oils (e.g., cottonseed,groundnut, corn, germ, olive, castor, and sesame oils), glycerol,tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid estersof sorbitan, and mixtures thereof. Besides inert diluents, the oralcompositions can include adjuvants such as wetting agents, emulsifyingand suspending agents, sweetening, flavoring, and perfuming agents. Incertain embodiments for parenteral administration, the conjugates of theinvention are mixed with solubilizing agents such as Cremophor™,alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins,polymers, and mixtures thereof.

Injectable preparations, for example, sterile injectable aqueous oroleaginous suspensions can be formulated according to the known artusing suitable dispersing or wetting agents and suspending agents. Thesterile injectable preparation can be a sterile injectable solution,suspension or emulsion in a nontoxic parenterally acceptable diluent orsolvent, for example, as a solution in 1,3-butanediol. Among theacceptable vehicles and solvents that can be employed are water,Ringer's solution, U.S.P. and isotonic sodium chloride solution. Inaddition, sterile, fixed oils are conventionally employed as a solventor suspending medium. For this purpose any bland fixed oil can beemployed including synthetic mono- or diglycerides. In addition, fattyacids such as oleic acid are used in the preparation of injectables.

The injectable formulations can be sterilized, for example, byfiltration through a bacterial-retaining filter, or by incorporatingsterilizing agents in the form of sterile solid compositions which canbe dissolved or dispersed in sterile water or other sterile injectablemedium prior to use.

In order to prolong the effect of a drug, it is often desirable to slowthe absorption of the drug from subcutaneous or intramuscular injection.This can be accomplished by the use of a liquid suspension ofcrystalline or amorphous material with poor water solubility. The rateof absorption of the drug then depends upon its rate of dissolutionwhich, in turn, may depend upon crystal size and crystalline form.Alternatively, delayed absorption of a parenterally administered drugform is accomplished by dissolving or suspending the drug in an oilvehicle.

Compositions for rectal or vaginal administration are typicallysuppositories which can be prepared by mixing the conjugates of thisinvention with suitable non-irritating excipients or carriers such ascocoa butter, polyethylene glycol or a suppository wax which are solidat ambient temperature but liquid at body temperature and therefore meltin the rectum or vaginal cavity and release the active ingredient.

Solid dosage forms for oral administration include capsules, tablets,pills, powders, and granules. In such solid dosage forms, the activeingredient is mixed with at least one inert, pharmaceutically acceptableexcipient or carrier such as sodium citrate or dicalcium phosphateand/or (a) fillers or extenders such as starches, lactose, sucrose,glucose, mannitol, and silicic acid, (b) binders such as, for example,carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone,sucrose, and acacia, (c) humectants such as glycerol, (d) disintegratingagents such as agar, calcium carbonate, potato or tapioca starch,alginic acid, certain silicates, and sodium carbonate, (e) solutionretarding agents such as paraffin, (f) absorption accelerators such asquaternary ammonium compounds, (g) wetting agents such as, for example,cetyl alcohol and glycerol monostearate, (h) absorbents such as kaolinand bentonite clay, and (i) lubricants such as talc, calcium stearate,magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate,and mixtures thereof. In the case of capsules, tablets and pills, thedosage form may comprise buffering agents.

Solid compositions of a similar type can be employed as fillers in softand hard-filled gelatin capsules using such excipients as lactose ormilk sugar as well as high molecular weight polyethylene glycols and thelike. The solid dosage forms of tablets, dragees, capsules, pills, andgranules can be prepared with coatings and shells such as entericcoatings and other coatings well known in the pharmaceutical formulatingart. They may optionally comprise opacifying agents and can be of acomposition that they release the active ingredient(s) only, orpreferentially, in a certain part of the intestinal tract, optionally,in a delayed manner. Examples of embedding compositions which can beused include polymeric substances and waxes. Solid compositions of asimilar type can be employed as fillers in soft and hard-filled gelatincapsules using such excipients as lactose or milk sugar as well as highmolecular weight polethylene glycols and the like.

The active ingredient can be in micro-encapsulated form with one or moreexcipients as noted above. The solid dosage forms of tablets, dragees,capsules, pills, and granules can be prepared with coatings and shellssuch as enteric coatings, release controlling coatings and othercoatings well known in the pharmaceutical formulating art. In such soliddosage forms the active ingredient can be admixed with at least oneinert diluent such as sucrose, lactose or starch. Such dosage forms maycomprise, as is normal practice, additional substances other than inertdiluents, e.g., tableting lubricants and other tableting aids such amagnesium stearate and microcrystalline cellulose. In the case ofcapsules, tablets and pills, the dosage forms may comprise bufferingagents. They may optionally comprise opacifying agents and can be of acomposition that they release the active ingredient(s) only, orpreferentially, in a certain part of the intestinal tract, optionally,in a delayed manner. Examples of embedding compositions which can beused include polymeric substances and waxes.

Dosage forms for topical and/or transdermal administration of a compoundof this invention may include ointments, pastes, creams, lotions, gels,powders, solutions, sprays, inhalants and/or patches. Generally, theactive ingredient is admixed under sterile conditions with apharmaceutically acceptable carrier and/or any needed preservativesand/or buffers as can be required. Additionally, the present inventioncontemplates the use of transdermal patches, which often have the addedadvantage of providing controlled delivery of an active ingredient tothe body. Such dosage forms can be prepared, for example, by dissolvingand/or dispensing the active ingredient in the proper medium.Alternatively or additionally, the rate can be controlled by eitherproviding a rate controlling membrane and/or by dispersing the activeingredient in a polymer matrix and/or gel.

Suitable devices for use in delivering intradermal pharmaceuticalcompositions described herein include short needle devices such as thosedescribed in U.S. Pat. Nos. 4,886,499; 5,190,521; 5,328,483; 5,527,288;4,270,537; 5,015,235; 5,141,496; and 5,417,662. Intradermal compositionscan be administered by devices which limit the effective penetrationlength of a needle into the skin, such as those described in PCTpublication WO 99/34850 and functional equivalents thereof. Jetinjection devices which deliver liquid vaccines to the dermis via aliquid jet injector and/or via a needle which pierces the stratumcorneum and produces a jet which reaches the dermis are suitable. Jetinjection devices are described, for example, in U.S. Pat. Nos.5,480,381; 5,599,302; 5,334,144; 5,993,412; 5,649,912; 5,569,189;5,704,911; 5,383,851; 5,893,397; 5,466,220; 5,339,163; 5,312,335;5,503,627; 5,064,413; 5,520,639; 4,596,556; 4,790,824; 4,941,880;4,940,460; and PCT publications WO 97/37705 and WO 97/13537. Ballisticpowder/particle delivery devices which use compressed gas to acceleratevaccine in powder form through the outer layers of the skin to thedermis are suitable. Alternatively or additionally, conventionalsyringes can be used in the classical mantoux method of intradermaladministration.

Formulations suitable for topical administration include, but are notlimited to, liquid and/or semi liquid preparations such as liniments,lotions, oil in water and/or water in oil emulsions such as creams,ointments and/or pastes, and/or solutions and/or suspensions.Topically-administrable formulations may, for example, comprise fromabout 1% to about 10% (w/w) active ingredient, although theconcentration of the active ingredient can be as high as the solubilitylimit of the active ingredient in the solvent. Formulations for topicaladministration may further comprise one or more of the additionalingredients described herein.

A pharmaceutical composition of the invention can be prepared, packaged,and/or sold in a formulation suitable for pulmonary administration viathe buccal cavity. Such a formulation may comprise dry particles whichcomprise the active ingredient and which have a diameter in the rangefrom about 0.5 to about 7 nanometers or from about 1 to about 6nanometers. Such compositions are conveniently in the form of drypowders for administration using a device comprising a dry powderreservoir to which a stream of propellant can be directed to dispersethe powder and/or using a self propelling solvent/powder dispensingcontainer such as a device comprising the active ingredient dissolvedand/or suspended in a low-boiling propellant in a sealed container. Suchpowders comprise particles wherein at least 98% of the particles byweight have a diameter greater than 0.5 nanometers and at least 95% ofthe particles by number have a diameter less than 7 nanometers.Alternatively, at least 95% of the particles by weight have a diametergreater than 1 nanometer and at least 90% of the particles by numberhave a diameter less than 6 nanometers. Dry powder compositions mayinclude a solid fine powder diluent such as sugar and are convenientlyprovided in a unit dose form.

Low boiling propellants generally include liquid propellants having aboiling point of below 65 ° F. at atmospheric pressure. Generally thepropellant may constitute 50 to 99.9% (w/w) of the composition, and theactive ingredient may constitute 0.1 to 20% (w/w) of the composition.The propellant may further comprise additional ingredients such as aliquid non-ionic and/or solid anionic surfactant and/or a solid diluent(which may have a particle size of the same order as particlescomprising the active ingredient).

Pharmaceutical compositions of the invention formulated for pulmonarydelivery may provide the active ingredient in the form of droplets of asolution and/or suspension. Such formulations can be prepared, packaged,and/or sold as aqueous and/or dilute alcoholic solutions and/orsuspensions, optionally sterile, comprising the active ingredient, andmay conveniently be administered using any nebulization and/oratomization device. Such formulations may further comprise one or moreadditional ingredients including, but not limited to, a flavoring agentsuch as saccharin sodium, a volatile oil, a buffering agent, a surfaceactive agent, and/or a preservative such as methylhydroxybenzoate. Thedroplets provided by this route of administration may have an averagediameter in the range from about 0.1 to about 200 nanometers.

Formulations described herein as being useful for pulmonary delivery areuseful for intranasal delivery of a pharmaceutical composition of theinvention. Another formulation suitable for intranasal administration isa coarse powder comprising the active ingredient and having an averageparticle from about 0.2 to 500 micrometers. Such a formulation isadministered by rapid inhalation through the nasal passage from acontainer of the powder held close to the nares.

Formulations for nasal administration may, for example, comprise fromabout as little as 0.1% (w/w) and as much as 100% (w/w) of the activeingredient, and may comprise one or more of the additional ingredientsdescribed herein. A pharmaceutical composition of the invention can beprepared, packaged, and/or sold in a formulation for buccaladministration. Such formulations may, for example, be in the form oftablets and/or lozenges made using conventional methods, and maycontain, for example, 0.1 to 20% (w/w) active ingredient, the balancecomprising an orally dissolvable and/or degradable composition and,optionally, one or more of the additional ingredients described herein.Alternately, formulations for buccal administration may comprise apowder and/or an aerosolized and/or atomized solution and/or suspensioncomprising the active ingredient. Such powdered, aerosolized, and/oraerosolized formulations, when dispersed, may have an average particleand/or droplet size in the range from about 0.1 to about 200 nanometers,and may further comprise one or more of the additional ingredientsdescribed herein.

A pharmaceutical composition of the invention can be prepared, packaged,and/or sold in a formulation for ophthalmic administration. Suchformulations may, for example, be in the form of eye drops including,for example, a 0.1/1.0% (w/w) solution and/or suspension of the activeingredient in an aqueous or oily liquid carrier. Such drops may furthercomprise buffering agents, salts, and/or one or more other of theadditional ingredients described herein. Otheropthalmically-administrable formulations which are useful include thosewhich comprise the active ingredient in microcrystalline form and/or ina liposomal preparation. Ear drops and/or eye drops are contemplated asbeing within the scope of this invention.

Although the descriptions of pharmaceutical compositions provided hereinare principally directed to pharmaceutical compositions which aresuitable for administration to humans, it will be understood by theskilled artisan that such compositions are generally suitable foradministration to animals of all sorts. Modification of pharmaceuticalcompositions suitable for administration to humans in order to renderthe compositions suitable for administration to various animals is wellunderstood, and the ordinarily skilled veterinary pharmacologist candesign and/or perform such modification with ordinary experimentation.

Compounds provided herein are typically formulated in dosage unit formfor ease of administration and uniformity of dosage. It will beunderstood, however, that the total daily usage of the compositions ofthe present invention will be decided by the attending physician withinthe scope of sound medical judgment. The specific therapeuticallyeffective dose level for any particular subject or organism will dependupon a variety of factors including the disease being treated and theseverity of the disorder; the activity of the specific active ingredientemployed; the specific composition employed; the age, body weight,general health, sex and diet of the subject; the time of administration,route of administration, and rate of excretion of the specific activeingredient employed; the duration of the treatment; drugs used incombination or coincidental with the specific active ingredientemployed; and like factors well known in the medical arts.

The compounds and compositions provided herein can be administered byany route, including enteral (e.g., oral), parenteral, intravenous,intramuscular, intra-arterial, intramedullary, intrathecal,subcutaneous, intraventricular, transdermal, interdermal, rectal,intravaginal, intraperitoneal, topical (as by powders, ointments,creams, and/or drops), mucosal, nasal, bucal, sublingual; byintratracheal instillation, bronchial instillation, and/or inhalation;and/or as an oral spray, nasal spray, and/or aerosol. Specificallycontemplated routes are oral administration, intravenous administration(e.g., systemic intravenous injection), regional administration viablood and/or lymph supply, and/or direct administration to an affectedsite. In general the most appropriate route of administration willdepend upon a variety of factors including the nature of the agent(e.g., its stability in the environment of the gastrointestinal tract),and/or the condition of the subject (e.g., whether the subject is ableto tolerate oral administration).

The exact amount of a compound required to achieve an effective amountwill vary from subject to subject, depending, for example, on species,age, and general condition of a subject, severity of the side effects ordisorder, identity of the particular compound(s), mode ofadministration, and the like. The desired dosage can be delivered threetimes a day, two times a day, once a day, every other day, every thirdday, every week, every two weeks, every three weeks, or every fourweeks. In certain embodiments, the desired dosage can be delivered usingmultiple administrations (e.g., two, three, four, five, six, seven,eight, nine, ten, eleven, twelve, thirteen, fourteen, or moreadministrations).

In certain embodiments, an effective amount of a compound foradministration one or more times a day to a 70 kg adult human maycomprise about 0.0001 mg to about 3000 mg, about 0.0001 mg to about 2000mg, about 0.0001 mg to about 1000 mg, about 0.001 mg to about 1000 mg,about 0.01 mg to about 1000 mg, about 0.1 mg to about 1000 mg, about 1mg to about 1000 mg, about 1 mg to about 100 mg, about 10 mg to about1000 mg, or about 100 mg to about 1000 mg, of a compound per unit dosageform.

In certain embodiments, the compounds of the invention may be at dosagelevels sufficient to deliver from about 0.001 mg/kg to about 100 mg/kg,from about 0.01 mg/kg to about 50 mg/kg, preferably from about 0.1 mg/kgto about 40 mg/kg, preferably from about 0.5 mg/kg to about 30 mg/kg,from about 0.01 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to about10 mg/kg, and more preferably from about 1 mg/kg to about 25 mg/kg, ofsubject body weight per day, one or more times a day, to obtain thedesired therapeutic effect.

It will be appreciated that dose ranges as described herein provideguidance for the administration of provided pharmaceutical compositionsto an adult. The amount to be administered to, for example, a child oran adolescent can be determined by a medical practitioner or personskilled in the art and can be lower or the same as that administered toan adult.

It will be also appreciated that a compound or composition, as describedherein, can be administered in combination with one or more additionaltherapeutically active agents. The compounds or compositions can beadministered in combination with additional therapeutically activeagents that improve their bioavailability, reduce and/or modify theirmetabolism, inhibit their excretion, and/or modify their distributionwithin the body. It will also be appreciated that the therapy employedmay achieve a desired effect for the same disorder, and/or it mayachieve different effects.

The compound or composition can be administered concurrently with, priorto, or subsequent to, one or more additional therapeutically activeagents. In general, each agent will be administered at a dose and/or ona time schedule determined for that agent. In will further beappreciated that the additional therapeutically active agent utilized inthis combination can be administered together in a single composition oradministered separately in different compositions. The particularcombination to employ in a regimen will take into account compatibilityof the inventive compound with the additional therapeutically activeagent and/or the desired therapeutic effect to be achieved. In general,it is expected that additional therapeutically active agents utilized incombination be utilized at levels that do not exceed the levels at whichthey are utilized individually. In some embodiments, the levels utilizedin combination will be lower than those utilized individually.

Exemplary additional therapeutically active agents include, but are notlimited to, anti-cancer agents, anti-diabetic agents, anti-inflammatoryagents, immunosuppres sant agents, and a pain-relieving agent.Therapeutically active agents include small organic molecules such asdrug compounds (e.g., compounds approved by the U.S. Food and DrugAdministration as provided in the Code of Federal Regulations (CFR)),peptides, proteins, carbohydrates, monosaccharides, oligosaccharides,polysaccharides, nucleoproteins, mucoproteins, lipoproteins, syntheticpolypeptides or proteins, small molecules linked to proteins,glycoproteins, steroids, nucleic acids, DNAs, RNAs, nucleotides,nucleosides, oligonucleotides, antisense oligonucleotides, lipids,hormones, vitamins, and cells.

Also encompassed by the invention are kits (e.g., pharmaceutical packs).The kits provided may comprise an inventive pharmaceutical compositionor compound and a container (e.g., a vial, ampule, bottle, syringe,and/or dispenser package, or other suitable container). In someembodiments, provided kits may optionally further include a secondcontainer comprising a pharmaceutical excipient for dilution orsuspension of an inventive pharmaceutical composition or compound. Insome embodiments, the inventive pharmaceutical composition or compoundprovided in the container and the second container are combined to formone unit dosage form.

Thus, in one aspect, provided are kits for preventing and/or treating adisease of a subject. In certain embodiments, the kits include a firstcontainer comprising a compound, or a pharmaceutically acceptable salt,solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer,isotopically labeled derivative, prodrug, and composition thereof; andan instruction for administering the compound, or a pharmaceuticallyacceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer,stereoisomer, isotopically labeled derivative, prodrug, and compositionthereof, to a subject to prevent or treat a JNK-associated disease. Incertain embodiments, the kits include a first container comprising a JNKinhibitor. In certain embodiments, the kits include a first containercomprising an irreversible JNK inhibitor. In certain embodiments, thekits include a first container comprising a compound of the presentinvention. In certain embodiments, the kits include a first containercomprising a compound of the present invention. In certain embodiments,the kits include a first container comprising a compound describedherein. In certain embodiments, the kits include a first containercomprising a compound selected from the group consisting of JNK-IN-5,JNK-IN-6, JNK-IN-7, JNK-IN-8, JNK-IN-9, JNK-IN-10, JNK-IN-11, andJNK-IN-12. In certain embodiments, the kits include a first containercomprising a compound selected from the group consisting of THZ-2-117-1,THZ-2-118-1, THZ-2-140-2, THZ-2-142-1, THZ-2-143-1, THZ-2-144-1,THZ-2-145-1, THZ-2-147-1, THZ-2-148-1, THZ-3-06-1, THZ-3-07-1,THZ-3-11-1, THZ-3-30-1, THZ-3-39-1, and THZ-3-46-1.

In certain embodiments, the kits are used for preventing and/or treatingdiseases associated with JNK kinase activity. In certain embodiments,the kits are used for preventing and/or treating a proliferativedisease. In certain embodiments, the kits are used for preventing and/ortreating cancer. In certain embodiments, the kits are used forpreventing and/or treating a benign neoplasm. In certain embodiments,the kits are used for preventing and/or treating a neurodegenerativedisease. In certain embodiments, the kits are used for preventing and/ortreating a metabolic disorder. In certain embodiments, the kits are usedfor preventing and/or treating an inflammatory disease. In certainembodiments, the kits are used for preventing and/or treating acardiovascular disease.

Methods of Treatment

The present invention provides methods for the prevention and treatmentof various diseases, e.g., neurodegenerative diseases, metabolicdisorders, inflammatory diseases, cardiovascular diseases, andproliferative diseases (e.g., cancer and benign neoplasms).

In certain embodiments, the methods of the present invention compriseadministering to a subject in need thereof an effective amount of acompound of the present invention, or a pharmaceutical compositionthereof.

In certain embodiments, the effective amount is a therapeuticallyeffective amount. In certain embodiments, the effective amount is aprophylactically effective amount.

In certain embodiments, the subject administered the inventive compound,or composition as described herein, is an animal. The animal may be ofeither sex and may be of any stage of development. In certainembodiments, the animal is a mammal. In certain embodiments, the subjectis a human. In certain embodiments, the subject is a domesticatedanimal, such as a dog, cat, cow, pig, horse, sheep, or goat. In certainembodiments, the subject is a companion animal such as a dog or cat. Incertain embodiments, the subject is a livestock animal such as a cow,pig, horse, sheep, or goat. In certain embodiments, the subject is a zooanimal. In another embodiment, the subject is a research animal such asa rodent (e.g., mouse, rat), dog, pig, or non-human primate. In certainembodiments, the subject is a non-human, genetically engineered animal.In certain embodiments, the subject is a non-human transgenic animal,such as a transgenic mouse or transgenic pig.

In certain embodiments, the disease is a proliferative disease, e.g.,cancer. In certain embodiments, the disease is benign neoplasm. Incertain embodiments, the disease is a neurodegenerative disease. Incertain embodiments, the disease is stroke. In certain embodiments, thedisease is Parkinson's disease. In certain embodiments, the disease isAlzheimer's disease. In certain embodiments, the disease is a metabolicdisorder. In certain embodiments, the disease is diabetes. In certainembodiments, the disease is an inflammatory disease. In certainembodiments, the disease is a cardiovascular disease, e.g., stroke.

In certain embodiments, the methods of the present invention compriseadministering to a subject with a proliferative disease (e.g., cancer)an effective amount of a compound of the present invention, or thepharmaceutical composition thereof. Exemplary cancers include, but arenot limited to, acoustic neuroma; adenocarcinoma; adrenal gland cancer;anal cancer; angiosarcoma (e.g., lymphangiosarcoma,lymphangioendotheliosarcoma, hemangiosarcoma); appendix cancer; benignmonoclonal gammopathy; biliary cancer (e.g., cholangiocarcinoma);bladder cancer; breast cancer (e.g., adenocarcinoma of the breast,papillary carcinoma of the breast, mammary cancer, medullary carcinomaof the breast); brain cancer [e.g., meningioma, glioblastomas, glioma(e.g., astrocytoma, oligodendroglioma), medulloblastoma]; bronchuscancer; carcinoid tumor; cervical cancer (e.g., cervicaladenocarcinoma); choriocarcinoma; chordoma; craniopharyngioma;colorectal cancer (e.g., colon cancer, rectal cancer, colorectaladenocarcinoma); connective tissue cancer; epithelial carcinoma;ependymoma; endothelio sarcoma (e.g., Kaposi's sarcoma, multipleidiopathic hemorrhagic sarcoma); endometrial cancer (e.g., uterinecancer, uterine sarcoma); esophageal cancer (e.g., adenocarcinoma of theesophagus, Barrett's adenocarinoma); Ewing sarcoma; eye cancer (e.g.,intraocular melanoma, retinoblastoma); familiar hypereosinophilia; gallbladder cancer; gastric cancer (e.g., stomach adenocarcinoma);gastrointestinal stromal tumor (GIST); germ cell cancer; head and neckcancer (e.g., head and neck squamous cell carcinoma, oral cancer (e.g.,oral squamous cell carcinoma), throat cancer (e.g., laryngeal cancer,pharyngeal cancer, nasopharyngeal cancer, oropharyngeal cancer));hematopoietic cancers (e.g., leukemia such as acute lymphocytic leukemia(ALL) (e.g., B-cell ALL, T-cell ALL), acute myelocytic leukemia (AML)(e.g., B-cell AML, T-cell AML), chronic myelocytic leukemia (CML) (e.g.,B-cell CML, T-cell CML), and chronic lymphocytic leukemia (CLL) (e.g.,B-cell CLL, T-cell CLL)]; lymphoma such as Hodgkin lymphoma (HL) (e.g.,B-cell HL, T-cell HL) and nonHodgkin lymphoma (NHL) (e.g., B-cell NHLsuch as diffuse large cell lymphoma (DLCL) (e.g., diffuse large Bcelllymphoma), follicular lymphoma, chronic lymphocytic leukemia/smalllymphocytic lymphoma (CLL/SLL), mantle cell lymphoma (MCL), marginalzone B-cell lymphomas (e.g., mucosa-associated lymphoid tissue (MALT)lymphomas, nodal marginal zone B-cell lymphoma, splenic marginal zoneB-cell lymphoma), primary mediastinal B-cell lymphoma, Burkitt lymphoma,lymphoplasmacytic lymphoma (i.e., Waldenstrom's macroglobulinemia),hairy cell leukemia (HCL), immunoblastic large cell lymphoma, precursorB-lymphoblastic lymphoma and primary central nervous system (CNS)lymphoma; and T-cell NHL such as precursor T-lymphoblasticlymphoma/leukemia, peripheral T-cell lymphoma (PTCL) (e.g., cutaneousT-cell lymphoma (CTCL) (e.g., mycosis fungiodes, Sezary syndrome),angioimmunoblastic T-cell lymphoma, extranodal natural killer T-celllymphoma, enteropathy type T-cell lymphoma, subcutaneouspanniculitis-like T-cell lymphoma, and anaplastic large cell lymphoma);a mixture of one or more leukemia/lymphoma as described above; andmultiple myeloma (MM)), heavy chain disease (e.g., alpha chain disease,gamma chain disease, mu chain disease); hemangioblastoma; hypopharynxcancer; inflammatory myofibroblastic tumors; immunocytic amyloidosis;kidney cancer (e.g., nephroblastoma a.k.a. Wilms' tumor, renal cellcarcinoma); liver cancer (e.g., hepatocellular cancer (HCC), malignanthepatoma); lung cancer (e.g., bronchogenic carcinoma, small cell lungcancer (SCLC), nonsmall cell lung cancer (NSCLC), adenocarcinoma of thelung); leiomyosarcoma (LMS); mastocytosis (e.g., systemic mastocytosis);muscle cancer; myelodysplastic syndrome (MDS); mesothelioma;myeloproliferative disorder (MPD) (e.g., polycythemia vera (PV),essential thrombocytosis (ET), agnogenic myeloid metaplasia (AMM) a.k.a.myelofibrosis (MF), chronic idiopathic myelofibrosis, chronic myelocyticleukemia (CML), chronic neutrophilic leukemia (CNL), hypereosinophilicsyndrome (HES)); neuroblastoma; neurofibroma (e.g., neurofibromatosis(NF) type 1 or type 2, schwannomatosis); neuroendocrine cancer (e.g.,gastroenteropancreatic neuroendoctrine tumor (GEP-NET), carcinoidtumor); osteosarcoma (e.g., bone cancer); ovarian cancer (e.g.,cystadenocarcinoma, ovarian embryonal carcinoma, ovarianadenocarcinoma); papillary adenocarcinoma; pancreatic cancer (e.g.,pancreatic andenocarcinoma, intraductal papillary mucinous neoplasm(IPMN), Islet cell tumors); penile cancer (e.g., Paget's disease of thepenis and scrotum); pinealoma; primitive neuroectodermal tumor (PNT);plasma cell neoplasia; paraneoplastic syndromes; intraepithelialneoplasms; prostate cancer (e.g., prostate adenocarcinoma); rectalcancer; rhabdomyosarcoma; salivary gland cancer; skin cancer [e.g.,squamous cell carcinoma (SCC), keratoacanthoma (KA), melanoma, basalcell carcinoma (BCC)]; small bowel cancer (e.g., appendix cancer); softtissue sarcoma (e.g., malignant fibrous histiocytoma (MFH), liposarcoma,malignant peripheral nerve sheath tumor (MPNST), chondrosarcoma,fibrosarcoma, myxosarcoma); sebaceous gland carcinoma; small intestinecancer; sweat gland carcinoma; synovioma; testicular cancer (e.g.,seminoma, testicular embryonal carcinoma); thyroid cancer (e.g.,papillary carcinoma of the thyroid, papillary thyroid carcinoma (PTC),medullary thyroid cancer); urethral cancer; vaginal cancer; and vulvarcancer (e.g., Paget's disease of the vulva).

In certain embodiments, the methods of the present invention compriseadministering to a subject with a benign neoplasm an effective amount ofa compound of the present invention, or the pharmaceutical compositionthereof.

In certain embodiments, the methods of the present invention compriseadministering to a subject with a neurodegenerative disease an effectiveamount of a compound of the present invention, or the pharmaceuticalcomposition thereof. Exemplary neurodegenerative diseases include, butare not limited to, multiple sclerosis. Parkinson's disease,Huntington's disease. amyotrophic lateral seleroqis. Alzheimer'sdisease. In certain embodiments, the methods of the present inventioncomprise administering to a subject with Parkinson's disease aneffective amount of a compound of the present invention, or thepharmaceutical composition thereof. In certain embodiments, the methodsof the present invention comprise administering to a subject withAlzheimer's disease an effective amount of a compound of the presentinvention, or the pharmaceutical composition thereof.

In certain embodiments, the methods of the present invention compriseadministering to a subject with a metabolic disorder (e.g., Type or IIdiabetes, or an obesity-related condition or complication thereof) aneffective amount of a compound of the present invention, or thepharmaceutical composition thereof. An “obesity-related condition” asused herein, includes, but is not limited to, a condition related toobesity, undesired weight gain (e.g., from medication-induced weightgain, from cessation of smoking) or an over-eating disorder (e.g., bingeeating, bulimia, compulsive eating, or a lack of appetite control eachof which can optionally lead to undesired weight gain or obesity).“Obesity” and “obese” as used herein, refers to class I obesity, classII obesity, class III obesity and pre-obesity (e.g., being“over-weight”) as defined by the World Health Organization.Obesity-related conditions include, but are not limited to, Type IIdiabetes mellitus; ischemic heart disease, arterial vascular disease,angina, myocardial infarction, stroke, migraines, congestive heartfailure, deep vein thrombosis, pulmonary embolism, gall stones,gastroesophagael reflux disease, obesity hypoventilation syndrome,erectile dysfunction, urinary incontinence, liver injury, and chronicrenal failure. In certain embodiments, the metabolic disorder isdiabetes. For example, in certain embodiments, the methods of thepresent invention comprise administering to a subject with diabetes(i.e., Type I or II diabetes) an effective amount of a compound of thepresent invention, or the pharmaceutical composition thereof.

In certain embodiments, the methods of the present invention compriseadministering to a subject with an inflammatory disease an effectiveamount of a compound of the present invention, or the pharmaceuticalcomposition thereof. Inflammatory disease refers to those diseases,disorders or conditions that are characterized by signs of pain (dolor,from the generation of noxious substances and the stimulation ofnerves), heat (calor, from vasodilatation), redness (rubor, fromvasodilatation and increased blood flow), swelling (tumor, fromexcessive inflow or restricted outflow of fluid), and/or loss offunction (functio laesa, which can be partial or complete, temporary orpermanent Inflammation takes on many forms and includes, but is notlimited to, acute, adhesive, atrophic, catarrhal, chronic, cirrhotic,diffuse, disseminated, exudative, fibrinous, fibrosing, focal,granulomatous, hyperplastic, hypertrophic, interstitial, metastatic,necrotic, obliterative, parenchymatous, plastic, productive,proliferous, pseudomembranous, purulent, sclerosing, seroplastic,serous, simple, specific, subacute, suppurative, toxic, traumatic,and/or ulcerative inflammation.

Exemplary inflammatory diseases include, but are not limited to,inflammation associated with acne, anemia (e.g., aplastic anemia,haemolytic autoimmune anaemia), asthma, arteritis (e.g., polyarteritis,temporal arteritis, periarteritis nodosa, Takayasu's arteritis),arthritis (e.g., crystalline arthritis, osteoarthritis, psoriaticarthritis, gouty arthritis, reactive arthritis, rheumatoid arthritis andReiter's arthritis), ankylosing spondylitis, amylosis, amyotrophiclateral sclerosis, autoimmune diseases, allergies or allergic reactions,atherosclerosis, bronchitis, bursitis, chronic prostatitis,conjunctivitis, Chagas disease, chronic obstructive pulmonary disease,cermatomyositis, diverticulitis, diabetes (e.g., type I diabetesmellitus, type 2 diabetes mellitus), a skin condition (e.g., psoriasis,eczema, burns, dermatitis, pruritus (itch)), endometriosis,Guillain-Barre syndrome, infection, ischaemic heart disease, Kawasakidisease, glomerulonephritis, gingivitis, hypersensitivity, headaches(e.g., migraine headaches, tension headaches), ileus (e.g.,postoperative ileus and ileus during sepsis), idiopathicthrombocytopenic purpura, interstitial cystitis (painful bladdersyndrome), gastrointestinal disorder (e.g., selected from peptic ulcers,regional enteritis, diverticulitis, gastrointestinal bleeding,eosinophilic gastrointestinal disorders (e.g., eosinophilic esophagitis,eosinophilic gastritis, eosinophilic gastroenteritis, eosinophiliccolitis), gastritis, diarrhea, gastroesophageal reflux disease (GORD, orits synonym GERD), inflammatory bowel disease (IBD) (e.g., Crohn'sdisease, ulcerative colitis, collagenous colitis, lymphocytic colitis,ischaemic colitis, diversion colitis, Behcet's syndrome, indeterminatecolitis) and inflammatory bowel syndrome (IBS)), lupus, multiplesclerosis, morphea, myeasthenia gravis, myocardial ischemia, nephroticsyndrome, pemphigus vulgaris, pernicious aneaemia, peptic ulcers,polymyositis, primary biliary cirrhosis, neuroinflammation associatedwith brain disorders (e.g., Parkinson's disease, Huntington's disease,and Alzheimer's disease), prostatitis, chronic inflammation associatedwith cranial radiation injury, pelvic inflammatory disease, reperfusioninjury, regional enteritis, rheumatic fever, systemic lupuserythematosus, schleroderma, scierodoma, sarcoidosis,spondyloarthopathies, Sjogren's syndrome, thyroiditis, transplantationrejection, tendonitis, trauma or injury (e.g., frostbite, chemicalirritants, toxins, scarring, burns, physical injury), vasculitis,vitiligo and Wegener's granulomatosis.

In certain embodiments, the methods of the present invention compriseadministering to a subject with a cardiovascular disease an effectiveamount of a compound of the present invention, or the pharmaceuticalcomposition thereof. Exemplary cardiovascular diseases include, but arenot limited to, hypertension, circulatory shock, myocardial reperfusioninjury, stroke, and atherosclerosis. In certain embodiments, the methodsof the present invention comprise administering to a subject with strokean effective amount of a compound of the present invention, or thepharmaceutical composition thereof.

In certain embodiments, the disease is a disease associated with JNKactivity, e.g., a disease associated with aberrant or unwanted JNKactivity. For example, in certain embodiments, the disease results fromincreased JNK activity. In certain embodiments, the methods of thepresent invention comprise administering to a subject with aJNK-associated disease an effective amount of a compound of the presentinvention, or a pharmaceutical composition thereof. Inhibition of JNK1is associated with treatment of cancer, diabetes, and inflammatorydiseases (e.g., inflammation). Increased JNK1 activity is alsoassociated with obesity, i.e., inhibition of JNK1 or mouse knockout hasbeen found to increase insulin sensitivity. Inhibition of JNK3 isassociated with the treatment of neurodegenerative diseases. SeeKyriakis et al., 2001; Zhang et al., 2005; and Hunot et al., 2004 fordiscussions of the association of JNK with various neurodegenerativediseases, e.g., Parkinson's and Alzheimer's diseases.

CDK7 is also called CDK catalytic kinase which usually catalyze the CDK1and CDK2 for the phosphorylation of their substrate. For CDK1 and CDK2,they are activated in many cancers, e.g., colon cancer, liver cancer,and breast cancer. CDK7 is known to be responsible at least for RNAP IISer 2 and Ser 5 phosphorylation. CDK7 has a lysine which has a verysimilar location as cysteine in JNK, and it envisioned that active JNKinhibitors of the present invention will also be active CDK7 inhibitors.Thus, in certain embodiments, the methods of the present inventioncomprise administering to a subject with a CDK7-associated disease aneffective amount of a compound of the present invention, or apharmaceutical composition thereof.

In certain embodiments, the methods of the present invention compriseadministering to a subject with an IRAK1/4-associated disease aneffective amount of a compound of the present invention, or apharmaceutical composition thereof.

In certain embodiments, the methods of the present invention compriseadministering to a subject with an EGFR-associated disease an effectiveamount of a compound of the present invention, or a pharmaceuticalcomposition thereof.

In certain embodiments, the methods of the present invention compriseadministering to a subject with a DDR1/2-associated disease an effectiveamount of a compound of the present invention, or a pharmaceuticalcomposition thereof.

In certain embodiments, the methods of the present invention compriseadministering to a subject with a c-Kit-associated disease an effectiveamount of a compound of the present invention, or a pharmaceuticalcomposition thereof.

In certain embodiments, the methods of the present invention compriseadministering to a subject with a PDGFR-associated disease an effectiveamount of a compound of the present invention, or a pharmaceuticalcomposition thereof.

A proliferative disease may also be associated with inhibition ofapoptosis of a cell in a biological sample or subject. All types ofbiological samples described herein or known in the art are contemplatedas being within the scope of the invention. Apoptosis is the process ofprogrammed cell death. Inhibition of apoptosis may result inuncontrolled cell proliferation and, therefore, may cause proliferativediseases. In another aspect, the present invention provides methods ofinhibiting cell growth in a biological sample or subject by contactingwith the biological sample or administering to the subject an effectiveamount of a compound of the present invention, or a pharmaceuticalcomposition thereof.

In still another aspect, the present invention provides methods ofinducing apoptosis of a cell in a biological sample or a subject bycontacting with the biological sample or administering to the subject aneffective amount of a compound of the present invention, or apharmaceutical composition thereof.

The cell described herein may be an abnormal cell. The cell may be invitro or in vivo. In certain embodiments, the cell is a proliferativecell. In certain embodiments, the cell is a blood cell. In certainembodiments, the cell is a lymphocyte. In certain embodiments, the cellis a cancer cell. In certain embodiments, the cell is a benignneoplastic cell. In certain embodiments, the cell is an endothelialcell. In certain embodiments, the cell is an immune cell.

In certain embodiments, the compound is a JNK inhibitor. In certainembodiments, the compound is a JNK1 inhibitor. In certain embodiments,the compound is a JNK2 inhibitor. In certain embodiments, the compoundis a JNK3 inhibitor. In certain embodiments, the compound is a CDK7inhibitor. In certain embodiments, the compound is an IRAK1/4 inhibitor.In certain embodiments, the compound is an EGFR inhibitor. In certainembodiments, the compound is a DDR1/2 inhibitor. In certain embodiments,the compound is a c-Kit inhibitor. In certain embodiments, the compoundis a PDGFR inhibitor.

In certain embodiments, the compound is a compound of the presentinvention.

Another aspect of the invention relates to methods of screening alibrary of compounds to identify one or more compounds that are usefulin the treatment of a proliferative disease, in inhibiting cell growth,and/or in inducing apoptosis of a cell. In certain embodiments, thelibrary of compounds is a library of compounds of the present invention.The methods of screening a library include providing at least twodifferent compounds of the present invention, or pharmaceuticallyacceptable salts, solvates, hydrates, polymorphs, co-crystals,tautomers, stereoisomers, isotopically labeled derivatives, or prodrugsthereof, or pharmaceutical compositions thereof; and performing at leastone assay using the different compounds of the present invention, orpharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,or prodrugs thereof, or pharmaceutical compositions thereof, to detectone or more characteristics. In certain embodiments, the methods ofscreening a library include providing at least two different compoundsof the present invention, or pharmaceutically acceptable salts thereof,or pharmaceutical compositions thereof; and performing at least oneassay using the different compounds of the present invention, orpharmaceutically acceptable salts thereof, or pharmaceuticalcompositions thereof, to detect one or more characteristics. In certainembodiments, the characteristic is a characteristic associated withproliferative diseases. In certain embodiments, the characteristic is adesired characteristic. In certain embodiments, the desiredcharacteristic is usefulness in treating a proliferative disease, ininhibiting cell growth or cell proliferation, and/or in inducingapoptosis of a cell. In certain embodiments, the desired characteristicis anti-proliferation. In certain embodiments, the desiredcharacteristic is anti-cancer. In certain embodiments, the desiredcharacteristic is inhibition of a kinase. In certain embodiments, thedesired characteristic is inhibition of JNK. In certain embodiments, thedesired characteristic is inhibition of CDK7. In certain embodiments,the desired characteristic is inhibition of IRAK1/4. In certainembodiments, the desired characteristic is inhibition of EGFR. Incertain embodiments, the desired characteristic is inhibition of DDR1/2.In certain embodiments, the desired characteristic is inhibition ofc-Kit. In certain embodiments, the desired characteristic is inhibitionof PDGFR. The characteristic to be detected may also be an undesiredcharacteristic associated with the proliferative disease, cell growth orcell proliferation, and/or apoptosis of a cell. In certain embodiments,the undesired characteristic is induction of cell growth or cellproliferation. In certain embodiments, the undesired characteristic isinhibition of apoptosis of a cell.

The different compounds of the present invention may be provided fromnatural sources (see, e.g., Sternberg et al., Proc. Nat. Acad. Sci. USA,(1995) 92:1609-1613) or generated by synthetic methods such ascombinatorial chemistry (see, e.g., Ecker et al., Bio/Technology, (1995)13:351-360 and U.S. Pat. No. 5,571,902). In certain embodiments, thedifferent compounds are provided by liquid-phase or solution synthesis.In certain embodiments, the different compounds are provided bysolid-phase synthesis. In certain embodiments, the different compoundsare provided by a high-throughput, parallel, or combinatorial synthesis.In certain embodiments, the different compounds are provided by alow-throughput synthesis. In certain embodiments, the differentcompounds are provided by a one-pot synthesis. The different compoundsmay be provided robotically or manually. In certain embodiments, thestep of providing at least two different compounds of the presentinvention include arraying into at least two vessels at least twodifferent compounds of the present invention wherein the compounds arebound to solid supports, cleaving the compounds from the solid supports,and dissolving the cleaved compounds in a solvent. The solid supportsinclude, but do not limit to, beads (e.g., resin beads and magneticbeads), hollow fibers, solid fibers, plates, dishes, flasks, meshes,screens, and membranes. In certain embodiments, the solid supports arebeads. In certain embodiments, one solid support is capable ofsupporting at least 50 nmol of a compound. In certain embodiments, onesolid support is capable of supporting at least 100 nmol of a compound.In certain embodiments, one solid support is capable of supporting atleast 200 nmol of a compound. Each vessel may contain one or moresupport-bound compounds of the present invention. In certainembodiments, each vessel contains one support-bound compounds of thepresent invention. The solid supports and/or the compounds may belabeled with one or more labeling agents for the identification ordetection of the compounds. The vessels may be wells of a microtiterplate. The solvent may be an inorganic solvent, organic solvent, or amixture thereof. The steps of arraying, cleaving, and dissolving may beperformed robotically or manually.

Typically, the methods of screening a library of compounds involve atleast one assay. In certain embodiments, the assay is performed todetect one or more characteristics associated with the proliferativedisease described herein. The assay may be an immunoassay, such as asandwich-type assay, competitive binding assay, one-step direct test,two-step test, or blot assay. The step of performing at least one assaymay be performed robotically or manually. In certain embodiments, theactivity of a kinase is inhibited. In certain embodiments, the activityof JNK is inhibited. In certain embodiments, the activity of CDK isinhibited. In certain embodiments, the activity of CDK7 is inhibited. Incertain embodiments, the expression of a kinase, such as JNK and CDK(e.g., CDK7), is down-regulated. In certain embodiments, apoptosis of acell is induced.

Another aspect of the present invention relates to compounds describedtherein, or pharmaceutically acceptable salts, solvates, hydrates,polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeledderivatives, prodrugs, or compositions thereof, for use in treating aproliferative disease in a subject in need thereof.

Still another aspect of the present invention relates to compoundsdescribed therein, or pharmaceutically acceptable salts, solvates,hydrates, polymorphs, co-crystals, tautomers, stereoisomers,isotopically labeled derivatives, prodrugs, or compositions thereof, foruse in inhibiting cell growth in a biological sample or subject in needthereof.

In yet another aspect, the present invention provides compoundsdescribed therein, or pharmaceutically acceptable salts, solvates,hydrates, polymorphs, co-crystals, tautomers, stereoisomers,isotopically labeled derivatives, prodrugs, or compositions thereof, foruse in inducing apoptosis of a cell in a biological sample or subject inneed thereof.

EXAMPLES

In order that the invention described herein may be more fullyunderstood, the following examples are set forth. The synthetic andbiological examples described in this application are offered toillustrate the compounds, pharmaceutical compositions, and methodsprovided herein and are not to be construed in any way as limiting theirscope.

Example 1 Preparation of the Compounds General Synthetic Methods

The compounds provided herein can be prepared from readily availablestarting materials using the following general methods and procedures.See, e.g., Scheme 1 below. It will be appreciated that where typical orpreferred process conditions (i.e., reaction temperatures, times, moleratios of reactants, solvents, pressures, etc.) are given, other processconditions can also be used unless otherwise stated. Optimum reactionconditions may vary with the particular reactants or solvent used, butsuch conditions can be determined by those skilled in the art by routineoptimization procedures.

Additionally, as will be apparent to those skilled in the art,conventional protecting groups may be necessary to prevent certainfunctional groups from undergoing undesired reactions. The choice of asuitable protecting group for a particular functional group as well assuitable conditions for protection and deprotection are well known inthe art. For example, numerous protecting groups, and their introductionand removal, are described in Greene et al., Protecting Groups inOrganic Synthesis, Second Edition, Wiley, New York, 1991, and referencescited therein.

All solvents and reagents were used as obtained. ¹H NMR spectra wererecorded with a Varian Inova 600 NMR spectrometer and referenced todimethylsulfoxide. Chemical shifts are expressed in ppm. Mass spectrawere measured with Waters Micromass ZQ using an ESI source coupled to aWaters 2525 HPLC system operating in reverse mode with a Waters SunfireC₁₈ 5 μm, 4.6 mm×50 mm column. Purification of compounds was performedwith either a Teledyne ISCO CombiFlash Rf system or a Waters MicromassZQ preparative system. The purity was analyzed on the above-mentionedWaters LC-MS Symmetry (C₁₈ column, 4.6 mm×50 mm, 5 μM) using a gradientof 5-95% methanol in water containing 0.05% trifluoroacetic acid (TFA).

General processes for preparing compounds of the present invention,e.g., JNK-IN-5, JNK-IN-6, JNK-IN-7, JNK-IN-8, JNK-IN-9, JNK-IN-10,JNK-IN-11, and JNK-IN-12, are provided as further embodiments of theinvention and are illustrated in Schemes 1.

Each of the compounds shown in Scheme 1 may be designated a differentcompound number. Table 1 illustrates the alternative compounddesignation numbers of these compounds. For example, JNK-IN-5 andTHZ-2-117-1 are alternative compound numbers designating the samecompound.

TABLE 1 Alternative compound designation numbers JNK-IN-5 THZ-2-117-1JNK-IN-6 THZ-3-15-1 JNK-IN-7 THZ-2-118-1 JNK-IN-8 THZ-2-140-2 JNK-IN-9THZ-2-143-1 JNK-IN-10 THZ-2-145-1 JNK-IN-11 THZ-2-148-1 JNK-IN-12THZ-3-07-1

Buchwald Coupling

To a solution of 4-substituted-2-chloropyrimide in t-butanol was addedt-butyl-4-aminophenylcarbamate or t-butyl-3-aminophenylcarbamate (1.0equiv.), K₂CO₃ (1.0 equiv.), X-Phos (0.1 equiv.) and Pd₂(dba)₃. Afterheating at 90° C. for 6 h, the reaction mixture was diluted with amixture of chloroform and 2-propanol (4:1). The organic layer was washedwith water (3×), dried over MgSO₄, filtered and concentrated underreduced pressure. The resulting crude product was used for the next stepwithout further purification.

BOC Deprotection Using Trifluoroacetic Acid

To a stirred solution of the above crude product in CH₂Cl₂ was added TFAat room temperature. The reaction mixture was stirred for 2 h andconcentrated under reduced pressure. The resulting crude product waspurified by flash column chromatography with CH₂Cl₂/methanol (10/1) toprovide the title compound.

Preparation of Nitrobenzamide

The free amine obtained from the BOC deprotection step was dissolved inpyridine and nitrobenzoyl chloride (1.2 equiv.) was added to thissolution. After stirring for 2 h at 90° C., the reaction mixture wasconcentrated and the resulting crude product was used for the next stepwithout further purification.

Reduction of the Nitro Compound With SnCl₂

The nitro compound obtained from a reaction of the aniline andnitrobenzoyl chloride was suspended in ethyl acetate/methanol (5:1) andtreated with SnCl₂ (2.5 equiv.). After stirring for 2-5 h at 80° C., thereaction mixture was cooled to room temperature and poured intosaturated aqueous NaHCO₃. The mixture was stirred for 10 min and theaqueous phase was then extracted with chloroform and 2-propanol (4:1).The combined organic layer was washed with water and brine, dried overMgSO₄, filtered through a pad of celite and concentrated under reducedpressure. The resulting crude product was purified by flash columnchromatography with CH₂Cl₂/methanol (10/1) to provide the titlecompound.

Preparation of the Acrylamide

To a DMF solution of the aniline obtained in the reduction step wasadded N,N-diisopropylethylamine (1.2 equiv.). The reaction mixture wascooled to −60° C. and then treated with 4-chloro-but-2-enoyl chloride(5.0 equiv.) in CH₂Cl₂. The reaction mixture was stirred for 10 min at−60° C. and then treated with a solution of dimethylamine in THF. Thereaction mixture was then warmed to room temperature, stirred for 1 hand concentrated under reduced pressure. The resulting crude product waspurified by preparative HPLC to provide the title compound.

Analytical Data of Exemplary Compounds

JNK-IN-5: LC-MS: (M+H) 437, ¹H NMR (600 MHz, DMSO-d₆) 10.34 (s, 1H),10.19 (s, 1H), 9.71 (s, 1H), 9.33 (s, 1H), 8.72 (s, 1H), 8.57 (d, J=4.8Hz, 1H), 8.49 (d, J=4.8 Hz, 1H), 8.14 (s, 1H), 7.90 (d, J=9.0 Hz, 1H),7.76 (d, J=9.0 Hz, 2H), 7.68 (d, J=9.0 Hz, 2H), 7.63 (d, J=7.8 Hz, 1H),7.58 (m, 1H), 7.47 (m, 2H), 6.44 (m, 1H), 6.29 (d, J=16.2 Hz, 1H), 5.76(d, J=16.2 Hz, 1H).

JNK-IN-6: LC-MS(M+H) 439, ¹H NMR (600 MHz, DMSO-d₆) 10.12 (s, 1H0, 10.04(s, 1H), 9.72 (s, 1H), 9.33 (s, 1H), 8.74 (d, J=4.8 Hz, 1H), 8.58 (d,J=5.4 Hz, 1H), 8.55 (dt, J=6.0, 1.8 Hz, 1H), 8.07 (t, J=1.8 Hz, 1H),7.80 (d, J=7.2 Hz, 1H), 7.74 (d, J=9.6 Hz, 2H), 7.68 (d, J=9.6 Hz, 2H),7.64 (m, 1H), 7.58 (m, 1H), 7.47 (d, J=4.8 Hz, 1H), 7.41 (t, J=7.8 Hz,1H), 2.35 (q, J=7.8 Hz, 2H), 1.08 (t, J=7.8 Hz, 3H).

JNK-IN-7: LC-MS: (M+H) 494, ¹H NMR (600 MHz, DMSO-d₆) 10.53 (s, 1H),10.20 (s, 1H), 9.94 (b, 1H), 9.75 (s, 1H), 9.35 (s, 1H), 8.75 (d, J=4.8Hz, 1H), 8.59 (d, J=4.8 Hz, 1H), 8.56 (dt, J=4.8, 7.8 Hz, 1H), 8.17 (s,1H), 7.89 (d, J=9.0 Hz, 1H), 7.77 (d, J=9.0 Hz, 2H), 7.69 (d, J=9.0 Hz,2H), 7.65 (m, 2H), 7.49 (m, 2H), 6.76 (m, 1H), 6.48 (d, J=15.6 Hz, 1H),3.96 (d, J=6.0 Hz, 2H), 2.79 (s, 6H).

JNKIN-8: LC-MS: (M+H) 508, ¹H NMR (600 MHz, DMSO-d₆) 10.54 (s, 1H),10.20 (s, 1H), 9.24 (s, 1H), 8.95 (s, 1H), 8.70 (d, J=3.0 Hz, 1H), 8.47(d, J=4.8 Hz, 1H), 8.44 (d, J=7.8 Hz, 1H), 8.17 (s, 1H), 7.89 (d, J=7.8Hz, 1H), 7.77 (d, J=7.8 Hz, 1H), 7.63 (d, J=1.8 Hz, 1H), 7.49-7.44 (m,2H), 7.40 (d, J=5.4 Hz, 1H), 6.76 (m, 1H), 6.46 (d, J=15.6 Hz, 1H), 3.94(d, J=6.0 Hz, 2H), 2.79 (s, 6H), 2.23 (s, 3H).

JNK-IN-9: LC-MS: (M+H) 508, ¹H NMR (600 MHz, DMSO-d₆) 10.41, (s, 1H),10.22 (s, 1H), 9.71 (s, 1H), 9.33 (s, 1H), 8.73 (d, J=3.6 Hz, 1H), 8.58(d, J=5.4 Hz, 1H), 8.52 (d, J=7.8 Hz, 1H), 7.75 (m 3H), 7.67-7.61 (m,4H), 77.26 (d, J=8.4 Hz, 2H), 6.73 (m, 1H), 6.43 (d, J=15.6 Hz, 1H),3.94 (d, J=6.0 Hz, 2H), 2.79 (s, 6H), 2.32 (s, 3H).

JNK-IN-10: LC-MS (M+H) 508, ¹H NMR (600 MHz, DMSO-d₆), 10.12 (s, 1H),9.84 (s, 1H), 9.74 (s, 1H), 9.35 (s, 1H), 8.76 (d, J=4.2 Hz, 1H), 8.59(m, 2H), 8.05 (s, 1H), 7.75 (m, 3H), 7.67 (m, 3H), 7.47 (d, J=5.4 Hz,1H), 7.37 (d, J=8.4 Hz, 1H), 6.74 (m, 1H), 6.57 (d, J=15.6 Hz, 1H), 3.94(d, J=6.0 Hz, 2H), 2.79 (s, 6H), 2.27 (s, 3H).

JNK-IN-11: LC-MS: (M+H) 609, ¹H NMR (600 MHz, DMSO-d₆) 10.52 (s, 1H),10.17 (s, 1H), 9.53 (s, 1H), 8.81 (d, J=7.2 Hz, 1H), 8.47 (br, 1H), 8.22(d, J=5.4 Hz, 1H), 8.16 (s, 1H), 7.89 (d, J=8.4 Hz, 1H), 7.67 (d, J=7.8Hz, 1H), 7.59 (m, 6H), 7.47 (m, 5H), 7.11 (m, 1H), 6.77 (m, 1H), 6.45(m, 2H), 3.95 (d, J=6.6 Hz, 1 2H), 2.79 (s, 6H).

JNK-IN-12: LC-MS (M+H) 589, ¹H NMR (600 MHz, DMSO-d₆) 10.58 (s, 1H),10.43 (s, 1H), 10.12 (s, 1H), 8.23 (s, 1H), 7.93 (d, J=8.4 Hz, 2H), 7.84(br, 2H), 7.71 (d, J=8.4 Hz, 2H), 7.65 (m, 1H), 7.51 (m, 3H), 7.36 (br,1H), 7.22 (br, 1H), 6.78 (m, 1H), 6.52 (br, 1H), 6.47 (d, J=15.6 Hz,1H), 3.94 (d, J=6.0 Hz, 2H), 2.79 (s, 6H).

Example 2 Assays of the Compounds Intact Protein Analysis

For each analysis, about 100 pmol JNK protein +/− inhibitor (JNK-IN-7)was injected onto a self-packed reversed phase column ( 1/32″ O.D.×500μm I.D., 5 cm of POROS 10R2 resin). After desalting, protein was elutedwith an HPLC gradient (0-100% B in 4 minutes, A=0.2 M acetic acid inwater, B=0.2 M acetic acid in acetonitrile, and flow rate=10 μL/min)into a QTRAP mass spectrometer (AB Sciex, Toronto, Canada) or an LTQOrbitrap mass spectrometer (ThermoFisher Scientific, San Jose, Calif.).The QTRAP was operated in Q1 MS mode at unit resolution scanning at 2000amu/sec. LTQ OrbitrapMS spectra were acquired in centroid mode using theelectron multipliers for ion detection. Mass spectra were deconvolutedusing MagTran 1.03b2 software.

Protease Digestion and NanoLC/MS Analysis of Peptide Fragments

JNK-IN-7 treated JNK (25μg, about 620 pmol) was diluted with ammoniumbicarbonate buffer at pH 8.0 and then reduced for 30 min at 56° C. with10 mM DTT. After cooling for 5 min, the protein was alkylated with 22.5mM iodoacetamide for 30 min at room temperature in the dark and digestedovernight with 1.5 μg of trypsin at 37° C. In the morning, 1 μg of Glu-Cwas added, and the solution further incubated at 37° C. for 8 hr.Digested peptides (about 2 pmol) were injected onto a self-packedpre-column (4 cm POROS10R2) and eluted into the mass spectrometer (LTQOrbitrapVelos, ThermoFisher Scientific). Peptides were subjected to MS²by CAD (electron multiplier detection, relative collision energy 35%,q=0.25) as well as HCD (image current detection, resolution at m/z400=7500, and relative collision energy=35%).

Cell-Based Assays For c-Jun Phosphorylation

The cell based kinase assays for c-Jun phosphorylation carried out byusing the LanthaScreen™ c-Jun (1-79) HeLa cell line (Life Technologies,Carlsbad, Calif.) which stably express GFP-c-Jun 1-79 and GFP-ATF219-106, respectively. Phosphorylation was determined by measuring thetime resolved FRET (TR-FRET) between a terbium labeled phospho-c-Junspecific antibody and GFP. The cells were plated in white tissue culturetreated 384 well plates at a density of 10,000 cell per well in 32 μLassay medium (Opti-MEM®, supplemented with 0.5% charcoal/dextran-treatedFBS, 100 U/ml penicillin and 100 μg/ml streptomycin, 0.1 mM nonessentialamino acids, 1 mM sodium pyruvate, 25 mM Hepes, pH 7.3, and lackingphenol red). After overnight incubation, cells were pretreated for 90minutes with compound (at indicated concentration) diluted in 4 μL assaybuffer followed by 30 min of stimulation with 5 ng/ml of TNF-α in 4 μLassay buffer (final assay volume was 40 μl). The medium was then removedby aspiration, and the cells were lysed by adding 20 μl of lysis buffer(20 mM Tris-HCl, pH 7.6, 5 mM EDTA, 1% Nonidet P-40 substitute, 5 mMNaF, 150 mM NaCl, and 1:100 protease and phosphatase inhibitor mix,SIGMA P8340 and P2850, respectively). The lysis buffer included 2 nM ofthe terbium-labeled anti-c-Jun (pSer73) detection antibodies (LifeTechnologies). After allowing the assay to equilibrate for 60 minutes atroom temperature, TR-FRET emission ratios were determined on a BMGPherastar fluorescence plate reader (BMG Labtech, Cary, N.C.) using thefollowing parameters: excitation at 340 nm; emission at 520 nm and 490nm; 100 μs lag time; 200 μs integration time; and emission ratio=Em₅₂₀/Em₄₉₀. All data were analyzed and plotted using Graphpad Prism 4.

High Throughput Microscopy

Cells were plated at 7500 cells/well in 96-well microscopy plates(Corning) in recommended media for 24 hours, and then starved in medialacking serum for 16 hours. Cells were pre-treated for 180 minutes with10-fold stock solutions of JNK inhibitors and for 10 min with controlcompounds MK2206, PD0325901, SB239063, KIN040, and KIN208 and treatedwith 10-fold stock solutions of IGF-1, IL-6, TNF-α (all PeproTech), oranisomycin for 60 minutes. Cells were fixed in 2% paraformaldehyde for10 min at room temperature and washed with PBS-T (Phosphate BufferedSaline, 0.1% Tween 20). Cells were permeabilized in methanol for 10 minat room temperature, washed with PBS-T, and blocked in Odyssey BlockingBuffer (LI-COR Biosciences) for 1 hour at room temperature. Cells wereincubated overnight at 4° C. with antibody specific forErk1/2(pT202/pY204), Akt(pS473), c-Jun(pS73), pP38(T180/Y182) andpSTAT3(Y705) (Cell Signaling Technology), pRSK1(S380) and pMSK1(S376)(Epitomics), and NF-κB (Santa Cruz Biotechnology) diluted 1:400 inOdyssey Blocking Buffer. Cells were washed three times in PBS-T andincubated with rabbit-specific secondary antibody labeled with AlexaFluor 647 (Invitrogen) diluted 1:2000 in Odyssey Blocking Buffer. Cellswere washed once in PBS-T and once in PBS and incubated in 250 ng/mlHoechst 33342 (Invitrogen) and 1:1000 Whole Cell Stain (blue; ThermoScientific) solution. Cells were washed twice with PBS and imaged in animageWoRx high-throughput microscope (Applied Precision). Data wereplotted using DataPflex.

Binding Kinetics Assay

A375 cells (ATCC® CRL-1619™) were pre-treated with 1μM compound for theindicated amounts of time. Remove the medium and wash 3 times with PBS.Resuspend the cell pellet with 1 mL Lysis Buffer (1% NP-40, 1% CHAPS, 25mM Tris, 150 mM NaCl, Phosphatase Inhibitor Cocktail, Roche 04906845001,and Protease Inhibitor Cocktail Roche 11836170001). Rotate end-to-endfor 30 min at 4° C. Lysates were cleared by centrifugation at 14000 rpmfor 15 min in the Eppendorf. The cleared lysates gel filtered intoKinase Buffer (0.1% NP-40, 20 mM HEPES, 150 mM NaCl, PhosphataseInhibitor Cocktail, and Protease Inhibitor Cocktail) using Bio-Rad 10DGcolums. The total protein concentration of the gel-filtered lysateshould be around 5-15 mg/ml. Cell lysate was labeled with the probe fromActivX® at 5 μM for 1 hour. Samples were reduced with DTT, and cysteineswere blocked with iodoacetamide and gel filtered to remove excessreagents and exchange the buffer. Add 1 volume of 2× Binding Buffer (2%Triton-100, 1% NP-40, 2 mM EDTA, and 2× PBS) and 50 μL streptavidin beadslurry and rotate end-to-end for 2 hours, centrifuge at 7000 rpm for 2min. Wash 3 times with 1× Binding Buffer and 3 times with PBS. Add 30 μL1× sample buffer to beads, and heat samples at 95° C. for 10 min. Runsamples on an SDS-PAGE gel at 110 V. After transferred, the membrane wasimmunoblotted with JNK antibody (Cell signaling 9258).

Buffers

Lysis Buffer contained 50 mM Tris/HCl (pH 7.5), 1 mM EGTA, 1 mM EDTA, 1%(w/v) 1 mM sodium orthovanadate, 10 mM sodium β-glycerophosphate, 50 mMNaF, 5 mM sodium pyrophosphate, 0.27 M sucrose, 1 mM Benzamidine, and 2mM phenylmethanesulphonylfluoride (PMSF) and supplemented with 1% (v/v)Triton X-100. Kinase assay buffer contained 50 mM Tris/HCl (pH 7.5) and0.1 mM EGTA.

Cell Culture, Treatments and Cell Lysis

HEK-293 cells stably expressing Interleukin Receptor 1 (HEK293-IL1R)were cultured in Dulbecco's Modified Eagle's medium (DMEM) supplementedwith 10% FBS, 2 mM glutamine and 1× antimycotic/antibiotic solution.Cells were serum starved for 18 h before incubation with DMSO ordifferent inhibitors, stimulated with 2 μM anisomycin (Sigma) for 1 h,and lysates were clarified by centrifugation for 10 min at 16000 g and4° C.

Antibodies

Rabbit polyclonal antibodies against total pan JNK isoforms ((#9252),phospho-pan JNK isoforms (Thr183/Tyr185), (#4668), total p38 (#9212) orphospho-p38 MAPK (Thr180/Tyr182), (4631 resp.), total c-Jun (#9165),phospho-c-Jun (Ser63) (#9261), and phospho-MSK1 (Ser376) (#9591) werefrom Cell Signalling technology.

SDS-PAGE and Western Blot

Cell lysates (30 μg) were resolved by electrophoresis on SDSpolyacrylamide gels (10%) or Novex 4-12% gradient gels, andelectroblotted to nitrocellulose membranes. Membranes were blocked with5% skimmed milk (w/v) in 50 mM Tris/HCl (pH 7.5) 0.15 M NaCl, and 0.1%(v/v) Tween (TBST Buffer). Primary antibodies were used at aconcentration of 1 μg/ml, diluted in 5% skimmed milk in TBST, andincubated overnight at 4° C. Detection of immune-complexes was performedusing horseradish-peroxidase-conjugated secondary antibodies (Pierce)and an enhanced-chemiluminescence reagent (in-house).

JNK2 Kinase Assays

Wild type JNK2 or mutant JNK2[Cys116Ser] was activated in a reactionmixture containing 2 μM JNK2, 200 nM MKK4, 200 nM MKK7 in kinase assaybuffer containing 0.1 mM ATP, and 10 mM magnesium chloride. Afterincubation at 30 min at 30° C. the reaction mixture was snap frozen inaliquots. Activity of JNK2 was assessed in a total reaction volume of 50μl containing 200 nM activated wild type JNK or mutant JNK2[Cys116Ser],in kinase buffer containing 0.1 mM [γ-32P]ATP (about 500-1000 cpm/pmol),10 mM magnesium chloride, and 2 μM ATF2 (residues 19-96) as a substrate.Reactions were terminated by adding 20 mM EDTA. 40 μl of the reactionmixture was applied to P81 phosphocellulose paper which was washed in 50mM phosphoric acid and phosphorylated ATF2 peptide bound to p81 paperquantified by Cerenkov counting.

Results

The JNK family of kinases constitutes a central node in thestress-activated MAPK signaling pathway and may provide potentialtargets for future drugs to treat cancer, inflammatory diseases andneurological diseases. With the exception of a 9L analogue (FIG. 1;Crocker et al., 2011), achieving pharmacological inhibition of JNK inanimal models has to a large extent been hampered by the lack of potentand selective inhibitors with suitable pharmacokinetic properties. Toaddress these limitations, irreversible JNK inhibitors are developedthat covalently modify a conserved cysteine residue. The majoradvantages of this approach is that sustained target inhibition can beachieved with only transient exposure of the target to the inhibitorwhich reduces the need to achieve pharmacological properties that wouldallow for sustained drug levels in vivo (Singh et al., 2010). A furtheradvantage is that potent inhibition is completely dependent on covalentmodification and therefore mutation of the reactive cysteine residuecreates a version of JNK that are insensitive to the compounds. Thesemutant forms of JNK can then be used to establish the JNK-dependency ofany observed inhibitor induced phenotype which provides a powerfulcontrol for specificity.

Structure-based drug design was used to develop ATP-site directedcovalent inhibitors of JNK kinases that could target a unique cysteineconserved in all the JNK kinases. Cysteine-directed covalent inhibitorspossess a number of potential advantages relative to non-covalentinhibitors such as ability to control kinase selectivity using bothnon-covalent and covalent recognition of the kinase and the ability toexhibit prolonged pharmacodynamics despite competition with highendogenous intracellular ATP concentrations. Selective cysteine-directedcovalent inhibitors have been developed for a number of kinasesincluding Rsk (FMK) (Cohen et al., 2005; and Nguyen, 2008), FGFRs(FIIN-1) (Zhou et al., 2010), Mek (Schirmer et al., 2006), Nek2 (Heniseet al., 2011), and other kinases possessing a cysteine immediatelyproceeding the “DFG-motif” (hypothemycin and analogs) as well as severalundergoing clinical investigation as inhibitors of EGFR (HKI-272,BIBW2992, CI1033, and EKB569) and BTK (AVL-292, and PCI32765) (Singh etal., 2010). Despite these efforts, only four different cysteinepositions have been targeted in the ATP-site and there are at least 180kinases that possess a cysteine that could theoretically be targeted bysuitably designed inhibitors (Zhang et al., 2009). Here, provided in thepresent invention include the structure-based design, detailedbiochemical and cellular characterization, and crystal structureanalysis of JNK3 modified by covalent inhibitors that can irreversiblymodify a conserved cysteine residue in JNK.

Most currently reported cysteine-directed covalent inhibitors are fromthe “type-1” (Liu et al., 2006) inhibitor class: they bind to the kinasein an “active” conformation with the activation loop in a conformationconducive to substrate binding. It is speculated whether “type-2”inhibitors which bind kinases in an “inactive” state with the activationloop in a conformation that blocks substrate from binding might alsopresent a promising platform from which to design a new class ofcovalent inhibitors. Through an examination of kinases co-crystallizedwith type-2 inhibitors, it was noticed that both c-Kit (Leproult et al.,2011) and PDGFR possessed a cysteine immediately preceding the“DFG-motif” that marks the beginning of the activation loop and thatmight be exploited by a suitably designed type-2 inhibitor. It wasdecided to use the phenylaminopyrimidine core of imatinib as a scaffoldfor elaboration because this compound binds Abl, c-Kit and PDGFR in thetype-2 conformation and because it possesses favorable drug properties.Measurement of the distance between methylpiperidine moiety of imatiniband Cys788 in c-Kit (PDB: 1T46) (Mol et al., 2004) (FIG. 2A) inspiredthe effort to replace the methylpiperzine moiety with an electrophilicacrylamide bearing a water-solubility enhancing dimethylamino group togenerate JNK-IN-7 (FIG. 3). It was confirmed that these binding resultstranslated into single digit micromolar IC₅₀ for inhibition of JNKkinase activity using the “Z”-lyte assay format (Table 2). This resultwas unanticipated because despite the large number of JNK inhibitorsreported in the literature, there are no reports of “type-2” JNKinhibitors, and it was therefore not anticipated that imatinib couldbind to JNK in an extended “type-2” conformation. However, there are anumber of structurally related phenylaminopyrimidines such as 9L(Kamenecka et al., 2010) and 30 (Alam et al., 2007) (FIG. 1) that bindto JNK in a type-1 conformation, and it was speculated that perhapsJNK-IN-7 was binding in an analogous fashion to JNK. In addition, it washypothesized that imatinib might exploit an alternative “type-1”conformation when binding to JNK where the inhibitor assumes an U-shapedconfiguration as has been observed in a Syk-imatinib co-structure (PDB:1XBB) (Atwell et al., 2004), (FIG. 2B). If JNK-IN-7 were to recognizeJNK analogously to how imatinib binds to Syk, the acrylamide moiety ofJNK-IN-7 would be placed within covalent bond forming distance of Cys116of JNK1 and JNK2 and Cys154 of JNK3. To test these hypotheses, a numberof analogs of JNK-IN-7 were prepared (FIG. 3). Shown in Table 2 are theJNK-inhibition IC₅₀ values and c-Jun phosphorylation-inhibition (in Helaand A375 cells) values of these compounds.

TABLE 2 Biochemical IC₅₀ for JNK inhibitors against JNK1, JNK2, and JNK3and cellular EC₅₀ for inhibition of c-Jun phosphorylation in Hela andA375 cells Com- IC₅₀ (nM) p-c-Jun EC₅₀ (nM) pound JNK1 JNK2 JNK3 HelaA375 JNK-IN-5 2.11 1.93 0.96 118 32 JNK-IN-6 148    6760 1905 JNK-IN-71.54 1.99 0.75 130 244 JNK-IN-8 4.67 18.7  0.98 486 338 JNK-IN-9 0.5 104 117 JNK-IN- 0.5  173 141 10 JNK-IN- 1.34 0.5  0.5  48 8.6 11 JNK-IN-13    11.3  11    605 134 12 5A 10000*     200*    >10000 >10000 SP-110*    190*    7450 1985 600125 AS601245 150*    220*    70*   20252400 *Literature values.

Dramatic improvement in IC₅₀ was observed when a 1,4-dianiline and1,3-benzamide were incorporated as the linker segment between thepyrimidine and the acrylamide moiety as exemplified by JNK-IN-5 andJNK-IN-7. Molecular docking of JNK-IN-7 with JNK3 suggested that thissignificant improvement in potency was likely due to a more optimalplacement of the acrylamide relative to Cys154 which may result in moreefficient covalent bond formation (FIG. 4). Incubation of JNK-IN-7 andJNK3 followed by electrospray mass spectrometry revealed the addition ofa single molecule of inhibitor to the protein and labeling of Cys 154(FIGS. 5A to 5C).

In order to investigate the importance of covalent bond formation to thepotency of this class of inhibitor, JNK-IN-6 was prepared with anunreactive and approximately isosteric propyl amide group replacing theacrylamide of JNK-IN-5. As expected, this compound exhibited an almost100-fold less potent biochemical IC₅₀ on JNK1, 2, and 3 (Table 2). Asmall collection of analogs of JNK-IN-7 bearing modifications wasprepared that was expected to influence the selectivity relative toother kinases. Also prepared were three methylated analogs JNK-IN-8,JNK-IN-9, and JNK-IN-10, all of which retained the ability to potentlyinhibit JNK biochemical activity. The pyridine ring of JNK-IN-7 wasreplaced with substituents that had previously been reported in otherJNK inhibitors including a bulky group 2-phenylpyrazolo[1,5-a]pyridine(Alam et al., 2007) and benzothiazol-2-yl acetonitrile (Gaillard et al.,2005). The influence of these changes on kinase selectivity is discussedin detail below.

In order to validate the molecular modeling results and to provide abasis for further structure-based optimization efforts, JNK-IN-7 wasco-crystallized with JNK3 de novo using the same JNK3 protein reportedpreviously for 9L (Kamenecka et al., 2010) (FIG. 6 and Table 3). Theresulting 2.60 Å and 2.97 Å crystal structures were in good agreementwith the docking model described above. Continuous electron density wasvisible to Cys154 consistent with covalent bond formation (FIG. 7). Theinhibitor formed three hydrogen bonds with JNK3, two from theaminopyrimidine motif to the kinase hinge residues Leu148 and Met149 anda third from the amide NH to Asn152. This third hydrogen bond may beimportant for positioning the terminal ring and orienting the acrylamidemoiety proximal to Cys154 thereby facilitating covalent bond formation.The overall kinase conformation of JNK is remarkably similar to thereported 9L crystal structure (average RSMD 2.40 Å) (Kamenecka et al.,2010) with the kinase assuming an active conformation. This demonstratesthat the covalent inhibitor does not appear to trap an unusualconformation of the kinase. There is a small hydrophobic pocket adjacentto the aniline ortho position which may explain why there was tolerancefor the “flag” methyl group in JNK-IN-8 which provided a crucialselectivity determinant. The pyridine moiety binds in a hydrophobicpocket and did not optimally fill this space which was consistent withthe potency improvements realized by replacement with the largermoieties present in JNK-IN-11 and JNK-IN-12. Modification of theinhibitor in this region would clearly afford significant opportunitiesfor modulating both inhibitor potency and selectivity.

TABLE 3 Data collection and refinement statistics for a co-crystalstructure between JNK-IN-7 and the kinase domain of JNK3 (residues39-402) Space group P2₁2₁2 Cell dimensions (Å) a = 109.49, b = 156.26, c= 43.88, α = β = γ = 90 Asymmetric unit 2 Molecules Resolution (Å)¹156.26-2.97 (3.13-2.97) Unique reflections 16,326    I/σI¹ 13.2 (3.8)Completeness (%)¹ 100.0 (100.0) R_(sym) (I)^(1,2) 0.13 (0.49) RefinementResolution (Å)¹ 27.62-2.97 (3.17-2.97) Number of reflections 16,238   R_(free) ^(1,3) 27.13 (35.33) R_(cryst) ^(1,4) 20.01 (21.34) R.m.s. Bondlength (Å)    0.010 deviation Bond angle (°)    1.18  B-factor, average(Å²)    46.15  Number Protein   5536    of atoms Water   220    Ligand   86    (as modified cysteine) ¹Parentheses refer to statics for thehighest resolution shell.${{}_{}^{}{}_{}^{}} = {\sum\limits_{hkl}{\sum\limits_{i}{{{{I_{i}({hkl})} - \overset{\_}{I({hkl})}}}/{\sum\limits_{hkl}{\sum\limits_{i}{I_{i}({hkl})}}}}}}$³R_(free) is calculated with removal of 5.1% and 6.2% of the data forZG-10 and THZ-2-118-1, respectively, as the test sets at the beginningof refinements.${{}_{}^{}{}_{}^{}} = {\sum\limits_{hkl}{{{{{F_{obs}({hkl})}} - {{F_{calc}({hkl})}}}}/{\sum\limits_{hkl}{{F_{obs}({hkl})}}}}}$

In parallel with biochemical evaluation, the ability of the compounds toinhibit JNK activity in cells was investigated using two independentassays formats. This is a critical issue because there are severalreported JNK inhibitors with nanomolar biochemical potency thattranslate into micromolar cellular inhibitors. The most wellcharacterized direct phosphorylation substrate of JNK is thetranscription factor c-Jun. The first assay format is a high-throughput(HTS) compatible cellular assay capable of measuring changes inphosphorylation of c-Jun using the measurement of time resolvedfluorescence resonance energy transfer (TR-FRET) between a stablyexpressed GFP-c-Jun (1-79) fusion protein and a terbium labeled antipSer73 c-Jun antibody as readout (Robers et al., 2008; Carlson et al.,2009; and Stebbins et al., 2008). The second assay format consisted oftreating serum starved A375 cells with test compounds followed bystimulation of the JNK kinase pathway with anisomycin and monitoringc-Jun phosphorylation by confocal microscopy with an anti-phospho Ser73antibody (Millard et al., 2011; and Hendriks et al., 2010). With theexception of a few compounds, both assay formats provided a similarrank-order of IC₅₀'s for this compound series (Table 2). In agreementwith the biochemical assays, JNK-IN-5 also provided the break-through incellular potency and was capable of inhibiting of c-Jun phosphorylationwith an ICso of about 100 nM in HeLa cells and about 30 nM in A375cells. Introduction of the dimethyl group to yield JNK-IN-7 resulted ina 2-3-fold loss in potency for cellular JNK inhibition which was notpredicted based upon the enzymatic assay. Introduction of methyl groupsat the meta-position of the dianiline ring or to the meta and orthopositions of the benzamide resulted in compounds with cellular potencyin the hundreds of nanomolar range. JNK-IN-11, the most potent cellularinhibitor of JNK activity in this series, incorporated thephenylpyrazoleo[1,5-a]pyridine motif and possessed an IC₅₀ of about 30nM and about 10 nM in HeLa and A375 cells respectively. JNK-IN-6, thecompound incapable of covalent bond formation, possessed an IC₅₀ 50-foldhigher than its covalent analog JNK-IN-5 again underscoring therequirement for the acrylamide moiety to achieve potent cellularinhibition. In order to provide a direct comparison with published JNKinhibitors, SP600125, 5A, and AS601245 (FIG. 1) were tested in parallelin both assay formats. Surprisingly all these compounds exhibited IC₅₀'sin the micromolar range which suggests that covalent inhibition may berequired to observe potent inhibition under the conditions investigated.

In order to evaluate the kinetics with which JNK-IN-5 could covalentlymodify JNK in cells, a pulse-chase assay was developed. A375 cells weretreated with JNK-IN-5 for 1, 2, 3, 4, and 5 hours to allow for cellpenetration and labeling of intracellular targets. Cell lysates werethen prepared and labeled with ATP-biotin which contains a reactive acylphosphate anhydride that reacts non-specifically with the catalyticlysine of kinases including JNK (Patricelli et al., 2007). Streptavidinaffinity chromatography is then used to isolate all biotinylatedproteins and JNK protein is detected following SDS-PAGE and Westernblotting (FIG. 8). The amount of time that JNK-IN-5 must be incubatedwith cells to fully protect JNK from subsequent labeling by ATP-biotinprovides a measure of the rate of intracellular covalent bond formation.It took approximately three hours for JNK-IN-5 to modify JNK to anundetectable level by this assay format. As a negative control, thenon-covalent inhibitor JNK-IN-6 was subject to the same protocol and wasdemonstrated to be incapable of protecting JNK from labeling byATP-biotin.

The kinase selectivity of several key compounds was first evaluatedusing a chemical proteomic approach named KiNativ which detects 260kinases in A375 cells (ActivX Biosciences). To probe the intracellulartargets of the compounds, A375 cells were incubated with the inhibitorsand then looked for protection of labeling by an ATP-biotin probe thatnon-specifically labels conserved lysines on kinases and othernucleotide-dependent enzymes. This provided an important advantagerelative to the in vitro kinase selectivity profiling because in vitrothe short incubation times and presence of reactive thiols in thebuffers can potentially cause false negatives for acrylamide-modifiedkinase inhibitors. Treatment of A375 cells with 1 μM of four of theirreversible JNK inhibitors resulted in the identification of JNK as themost potent and common target (FIG. 9). In contrast, the reversibleinhibitor JNK-IN-6 did not inhibit JNK activity following the same livecell treatment. In addition to JNK1, JNK2, and JNK3, JNK-IN-7 also bindsto IRAK1, PIP5K3, PI3KC3, and PIP4K2C. Since cysteine-directed covalentkinase inhibitors will sometimes cross-react with kinases that containan equivalently placed cysteine, a sequence alignment was performed toidentify all kinases which have a cysteine near JNK1 Cys116 (FIG. 10).Amongst the 40 kinases revealed through this analysis, only IRAK1exhibited a detectable binding affinity to JNK-IN-7 based uponKinomeScan profiling. Since IRAK1 crystal structure is not available,the IRAK4 crystal structure (PDB: 3CGF) was examined which demonstratesthat Cys276 is potentially located in a similar location relative to thereactive Cys154 of JNK3. Therefore covalent modification of IRAK1 byJNK-IN-7 is a possibility and indeed biochemical kinase assay affordedan IC₅₀ of about 10 nM against IRAK1. To evaluate whether IRAK1 is abona fide intracellular target of JNK-IN-7, it was evaluated whether thecompound could inhibit the E3-ligase activity of pellino, which providesan indirect measure of inhibition of IRAK1 kinase activity in cells.JNK-IN-7 inhibited Interleukin 1-stimulated Pellino 1 E3 ligase activitybut required a relatively high concentration of 10 μM to achievecomplete inhibition (Goh et al., 2011). Sequence alignments do notreveal obvious cysteine residues that could be covalently modified inPIP3K3C, PIP4K2C, and PIP5K3, but further work will be required toevaluate whether these are indeed functional targets of JNK-IN-7.Although JNK-IN-7 is a relatively selective JNK inhibitor in cells,introduction of the “flag” methyl to yield JNK-IN-8 resulted in adramatic improvement in selectivity and eliminated binding to IRAK1,PIP3K3C, PIP4K2C, and PIP5K3. The dramatic selectivity improvement thatresults from introduction of this flag-methyl group has been previouslyreported for imatinib (Zimmermann et al., 1996). Replacement of thepyridine ring with bulkier substituents as exhibited by JNK-IN-11resulted in a broadening of the selectivity profile as well as furtherenhancing the potency for inhibition of c-Jun phosphorylation in cells.JNK-IN-11 binds potently to JNKs, p38, PIP5K3, ZAK, ZC2, PIP5K3, and CK1demonstrating that this compound class might be a valuable lead compoundto develop selective inhibitors of these potential alternative targets.JNK-IN-12, bearing a benzothiazol-2-yl acetonitrile moiety, displayed afurther broadened profile highlighting the value of KiNativ profiling inevaluating the full spectrum of intracellular targets.

To complement the KiNativ profiling, the in vitro kinase selectivity ofseveral key compounds was comprehensively evaluated by two complementaryapproaches: a kinase-binding assays against a panel of 442 distinctkinases using the KINOMEscan methodology (DiscoverX) and a standardradioactivity-based enzymatic assays against a panel of 124 kinases (TheNational Centre for Protein Kinase Profiling in Dundee). Based upon theKINOMEscan results, JNK-IN-7, JNK-IN-8, and JNK-IN-12 possessed highlyselective S scores (defined as the ratio number of kinases inhibitedmore than 90 percent at screening concentration of 1 μM) of 0.085,0.031, and 0.025, respectively (FIG. 11). For example, JNK-IN-7exhibited binding inhibition of 95% or more to approximately 14 kinasesat the concentration of 1.0 μM. It was attempted to confirm all thesepotent binding targets using either an enzymatic kinase assay or throughthe measurement of a dissociation constant to the kinase in question.JNK-IN-7 was confirmed to have a K_(d) or IC₅₀ of 100 nM or less againsteight additional kinases (FIG. 12). JNK-IN-7 was next tested for itsability to inhibit the enzymatic activity of a panel of 121 kinases at aconcentration of 1.0 μM. This analysis revealed 12 kinases that wereinhibited more than 80% relative to the DMSO control and follow-up IC₅₀determination revealed sub-200 nM IC₅₀ against of IRAK1, ERK8, and NUAK1(FIG. 13). JNK-IN-12 bearing a benzothiazol-2-yl acetonitrile in placeof the pyridine conferred an improved selectivity relative to JNK-IN-7.The KINOMEscan score for JNK-IN-12 was even smaller than JNK-IN-8, andfollow-up enzymatic assays on the potent targets revealed IC₅₀'s of37.6, 57.1, and 89.9 nM for IRAK1, HIPK4, and AKT2, respectively (FIG.12). This high in vitro selectivity however differed markedly from thelarge number of targets detected by KiNativ. The introduction ofphenylpyrazolo[1,5-a]pyridine to JNK-IN-11 resulted in a significantdecrease in kinase selectivity as assessed by KINOMEscan (Score=0.125)and more than 30 additional kinases including different mutants of EGFR,c-Kit, DDR1, and Gsk3b (FIGS. 12 and 13). Consistent with the KiNativprofiling, JNK-IN-8 also exhibited exceptional selectivity based uponKinomeScan and enzymatic profiling. Further biochemical and bindingassays failed to identify any target with an IC₅₀ or K_(d) of less than1.0 μM. Cumulatively these combined profiling technologies demonstratethat JNK-IN-8 is a remarkably selective covalent JNK inhibitor and isappropriate for interrogating JNK-dependent biological phenomena.

The profiling above provides an assessment of direct engagement withpotential targets but does not address further perturbations that maybeinduced as a consequence of these binding events. A confocalmicroscopy-based assay was therefore established using phospho-specificantibodies identical to that used to measure c-Jun phosphorylation,which would report on inhibition phosphorylation of sentinel nodes inother signaling pathways including Erk, p38, JNK, Akt, Stat, NFkB, andRsk by high throughput microscopy (Table 4 and FIGS. 14A to 14H)(Millard, et al., 2011). JNK-IN-7, JNK-IN-8, and JNK-IN-12 exhibitedonly on-pathway activity as monitored by inhibition of c-Junphosphorylation. JNK-IN-11 was the only compound found to haveoff-pathway activity as exemplified by its ability to potently blockphosphorylation of ERK, RSK1, MSK1, and p38 consistent with thesubstantially broadened kinase selectivity profile of this compound.Interestingly, JNK-IN-11 also provided the most complete inhibition ofc-Jun phosphorylation which is likely due to its ability to inhibitadditional pathways that ultimately signal to phospho-c-Jun.

TABLE 4 Cellular EC₅₀ values in nanomolar of four JNK inhibitors forinhibition of several signaling pathways as monitored by measuringinhibition of phosphorylation of Akt, Erk, Msk1, p38, RSK, STAT3, andc-Jun or NF-kB nuclear translocation using high-throughput microscopyNF-kB pAkt pErk pMSKl pP38 pRSK pSTAT3 pc-JunJNK-IN-7 >10000 >10000 >10000 >10000 >10000 >10000 >10000 285JNK-IN-8 >10000 >10000 >10000 >10000 >10000 >10000 >10000 425JNK-IN-11 >10000 >10000 19 14 15 20 >10000 <10JNK-IN-12 >10000 >10000 >10000 >10000 >10000 >10000 >10000 125

To further corroborate these results, what was also examined was theability of the compounds to inhibit phosphorylation of JNK, c-Jun, MSK1,and p38 in HEK293-ILR1 cells following stimulation by anisomycin bytraditional Western blotting (FIGS. 15A to 15C). All compounds, exceptthe JNK-IN-11, were capable of inhibiting c-Jun phosphorylation withoutinhibiting MSK1 and p38 phosphorylation. The inhibition was not reversedby removal of JNK-IN-8 from cell culture medium (FIGS. 16A and 16B). Theresults are in good agreement with the relative potencies establishedusing the immunostaining and kinase profiling approaches. Interestingly,a distinct reduction in electrophoretic mobility of JNK protein isapparent upon incubation with the inhibitors presumably as a consequenceof covalent modification by the inhibitors.

In order to investigate the extent to which the observed cellulareffects resulted from direct covalent modification of JNK1, JNK2, orJNK3 cysteine residues versus other potential intracellular targets,mutagenesis was used to engineer Cys to Ser mutant for JNK2. Cys116SerJNK2 JNK2 was purified, and it was confirmed that activated wild typeJNK2 and mutant JNK2[Cys116Ser] displayed similar K_(m) and V_(max)towards the ATF2 peptide substrate in vitro (FIG. 17). In the presenceof inhibitors, the mutation resulted in a 10-fold increase in IC₅₀ forinhibition of JNK activity by JNK-IN-11, and remarkably, at least a100-fold increase in IC₅₀ for JNK-IN-7 and JNK-IN-8 (FIG. 18). Overall,the results of the present invention demonstrate that JNK-IN-8 is anefficient, specific, and irreversible intracellular inhibitor of JNKkinase activity by a mechanism that depends on a conserved Cys in theATP-binding motif.

Comparative Data

Table 5 demonstrates the dramatic effects changing the orientation ofthe C and D ring have on JNK activity. For example, “para-meta”compounds of the present invention, i.e., compounds comprising para NHgroups on phenyl Ring C and meta NH(C═O) groups on phenyl Ring D, aresurprisingly more active than compounds having the opposite structuralconfiguration, i.e., “meta-para” compounds comprising meta-NHsubstituents on phenyl Ring C and para NH(C═O) groups on phenyl Ring D.

TABLE 5 IC₅₀ values in micromolars of compounds for certain kinasetargets E50/ Structure JNK1 JNK2 JNK3 A375 CDK7

  THZ-2-071-1 (meta-para) >10000   

  THZ-3-11-1 (para-meta)     0.897

  ZG-9 (meta-para) 1240   1720      184    5458

  JNK-IN-5 (para-meta)   2.11   1.93     0.96   32

  ZG-10 (meta-para)  809   1140      709    2400

  JNK-IN-7 (para-meta)   1.54   1.99     0.75   244

  ZG-6 (meta-para) 7780   4230      7750   

  JNK-IN-8 (para-meta)   4.67  18.7    <0.510  338

  THZ-2-102-1 (meta-para)  637    346      7110   

  THZ-3-30-1 (para-meta)   1.67   1.23     1.24  0.0755

Conclusion

Molecular docking of JNK-IN-7 into the crystal structures of JNK3,provided a rational basis for structure-guided design of the appropriatelinker-element that would serve to connect the phenylaminopyrimidinepharmacophore which is predicted to bind to the kinase-hinge segmentwith a reactive acrylamide moiety. It was discovered by the inventors ofthe present invention that the most critical feature to impart potentenzymatic and cellular JNK inhibition was for this linker segment tocontain a 1,4-disposition of the dianiline moiety and a 1,3-dispositionof terminal aminobenzoic acid moiety as exemplified by JNK-IN-7 andJNK-IN-8. A 2.97 Å co-structure between JNK-IN-7 and JNK3 fullycorroborated the molecular modeling and demonstrated covalent bondformation with residue Cys154 of JNK3. Extensive biochemical andcellular selectivity profiling allowed for identifying severaladditional kinase targets for JNK-IN-7 including IRAK1, MPSK1, NEK9,PIP3K3C, PIP4K2C, and PIP5K3. Interestingly most of these additionaltargets appear to require the acrylamide warhead to achieve efficientinhibition as they are not targeted by the non-acrylamide containinginhibitor JNK-IN-6. With the exception of IRAK1, these kinases do notappear to contain a reactive cysteine that is located in a similarposition to Cys154 of JNK3. This suggests that JNK-IN-7 may use adifferent conformation to recognize these kinases and thereby access analternative cysteine residue. Alternatively, JNK-IN-7 may form covalentadducts with reactive lysine residues. For example, the natural productinhibitor Wortmannin undergoes a Michael addition reaction with Lys833of Pi3K, albeit with a different electrophilic moiety. It has beenvalidated that JNK-IN-7 can indeed inhibit IRAK-1 dependent E3 ligaseactivity of pellino in cells albeit at higher concentrations (1-10 μM)and further optimization guided by the cell-based assay will be requiredto establish if more potent cellular inhibition of this target can beachieved (Goh et al., 2011). Two ways were discovered by the inventorsof the present invention to further enhance the kinase selectivity ofJNK-IN-7. The first was to introduce an ortho-methyl group which isanalogous to the “flag” methyl group of imatinib or the ortho-methoxygroup of the ALK inhibitor TAE684 (Galkin et al., 2007) and thepolo-kinase inhibitor BI-2356 (Kothe et al., 2007). This modificationwas exemplified by JNK-IN-8, and the crystal structure of JNK-IN-7predicts that this methyl group could possibly nestle into a small grovealong the hinge segment between Asp150 and Ala151 of JNK3. The secondwas to replace the pyridine moiety with a geometrically more complexbenzothiazol-2-yl acetonitrile moiety which was previously identified asa favorable pharmacophore for binding to the JNK ATP-site as exemplifiedby JNK-IN-12 (Gaillard et al., 2005). The functionality present in thisportion of the inhibitor which is predicted to bind in proximity to the“gatekeeper” methionine provides a critical selectivity determinant forthe inhibitors. For example, JNK-IN-11, which possesses a bulky2-phenylpyrazolo[1,5-a]pyridine group, displays a dramatically broadenedinhibition profile in both biochemical and cellular assays.

JNK-IN-12 appeared to bind to considerably more kinases based on theKiNativ technology relative to enzymatic or KinomeScan technology.Although there are several non overlapping targets detected by thesedifferent technologies, there may be cellular metabolism of thebenzothiazol-2-yl acetonitrile moiety to yield species that bind toadditional kinase targets. Further work will be required to establishwhether the additional targets detected by KiNativ for JNK IN 7,JNK-IN-11, and JNK-IN-12 are indeed covalently modified and whether bonafide potent cellular inhibition is achieved.

Covalent inhibitors are typically designed by rational modification ofscaffolds that are already potent non-covalent binders of the desiredtarget protein. For example, the anilinoquinazoline scaffold provides atemplate for highly potent covalent and non covalent inhibitors of EGFRkinase (Smaill et al., 2000). A second approach is to start fromrelatively low affinity non-covalent binders and to allow covalent bondformation to drive affinity toward the desired target. For example, thepyrrolopyimidine Rsk inhibitor CMK (Cohen et al., 2005) and theanilinopyrimidine T790M EGFR inhibitor WZ-4002 (Zhou et al., 2009) bothgain approximately 100-fold potency for their respective targets bycovalent bond formation. The covalent inhibitors described in this studyfall into this second category of requiring covalent bond formation inorder to achieve potent inhibition of JNK kinase activity. One majoradvantage of this second approach is that it is much easier to identifya relatively selective low affinity non-covalent scaffold as a startingpoint relative to a selective high affinity scaffold. The challenge withthe second approach is that one has to discover a scaffold that willallow presentation of the electrophile with the ideal geometry to allowfor covalent bond formation. This is especially true because theresidence time for a low affinity non-covalent compound is typicallyshort. As can be seen from the structure-activity relationship forJNK-IN-5 to 12, relatively minor changes can have dramatic consequencesto the potency of inhibition. This is in sharp contrast to the generalnotion that a covalent inhibitor will always be exceptionally potent.Intracellularly there is a kinetic competition for modification of thedesired target versus “off-targets” which maybe other proteins orengagement of cellular pathways that metabolize reactive electrophilies.In addition, proteins are continuously synthesized and degraded withvarying kinetics which can allow for regeneration of unmodified protein.Therefore an effective covalent inhibitor must label its target proteinrapidly relatively to competing labeling events and protein turn-over.

Two general approaches are favored to developing potent covalentinhibitors. The first is to generate small rationally designed librariesof electrophile modified inhibitors that can be used in cell-basedscreens to select for compounds with activity against the desiredtarget. Simple molecular modeling based on known ATP-site recognitionmodes can be used to select where on the scaffold to modify with anelectrophilic group. This approach was used to develop WZ-4002 a potentand selective inhibitor of the T790M “gatekeeper” mutation of EGFR. Thedisadvantage of this approach is that it requires considerable up-frontsynthetic effort and the cellular screening approach requires arelatively high efficiency inhibitor be present in the initial screeninglibrary. The second approach is to search for low affinity non-covalentscaffolds typically using a biochemical screening approach which allowsfor screening at high concentrations and then using structure-based drugdesign to prepare a small library of covalent inhibitors foroptimization. The advantage of this approach is that there is largecollection of known kinase inhibitors with known kinase selectivityprofiles. The disadvantage of this approach is that it can be difficultto predict which scaffold allows for the correct trajectory for theelectrophile relative to the protein nucleophile. Use of these and otherstrategies may provide an efficient means to generate first-in-classcovalent inhibitors for the large number of kinases containing suitablecysteine and possibly lysine residues.

It was demonstrated that the KiNativ profiling methodology is a powerfultool for discovering and guiding the optimization of new covalentinhibitors. First it allows for an unbiased screen of the majority ofavailable ATP-competitive targets in a cellular system of choice. Secondby assessing selectivity in a cellular context, the native kinaseconformation is accessed and the structure-activity relationships appearto correlate well with functional cellular assays. JNK-IN-8 achievespotent, selective, covalent, and irreversible inhibition of JNK in cellsthat reaches completion after approximately 3 hours (FIGS. 16A and 16B).It may be recommended that JNK-IN-8 be used at concentrations ofapproximately 1.0 μM and that preincubation time be approximately 3 h toinhibit cellular JNK activity.

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Other Embodiments

The foregoing has been a description of certain non-limiting embodimentsof the invention. Those of ordinary skill in the art will appreciatethat various changes and modifications to this description may be madewithout departing from the spirit or scope of the present invention, asdefined in the following claims.

All publications, including but not limited to journal articles, books,patents, and patent applications, cited in this specification are hereinincorporated by reference as if each individual publication werespecifically and individually indicated to be incorporated by referenceherein as though fully set forth.

Equivalents and Scope

In the claims articles such as “a,” “an,” and “the” may mean one or morethan one unless indicated to the contrary or otherwise evident from thecontext. Claims or descriptions that include “or” between one or moremembers of a group are considered satisfied if one, more than one, orall of the group members are present in, employed in, or otherwiserelevant to a given product or process unless indicated to the contraryor otherwise evident from the context. The invention includesembodiments in which exactly one member of the group is present in,employed in, or otherwise relevant to a given product or process. Theinvention includes embodiments in which more than one, or all of thegroup members are present in, employed in, or otherwise relevant to agiven product or process.

Furthermore, the invention encompasses all variations, combinations, andpermutations in which one or more limitations, elements, clauses, anddescriptive terms from one or more of the listed claims is introducedinto another claim. For example, any claim that is dependent on anotherclaim can be modified to include one or more limitations found in anyother claim that is dependent on the same base claim. Where elements arepresented as lists, e.g., in Markush group format, each subgroup of theelements is also disclosed, and any element(s) can be removed from thegroup. It should it be understood that, in general, where the invention,or aspects of the invention, is/are referred to as comprising particularelements and/or features, certain embodiments of the invention oraspects of the invention consist, or consist essentially of, suchelements and/or features. For purposes of simplicity, those embodimentshave not been specifically set forth in haec verba herein. It is alsonoted that the terms “comprising” and “containing” are intended to beopen and permits the inclusion of additional elements or steps. Whereranges are given, endpoints are included. Furthermore, unless otherwiseindicated or otherwise evident from the context and understanding of oneof ordinary skill in the art, values that are expressed as ranges canassume any specific value or subrange within the stated ranges indifferent embodiments of the invention, to the tenth of the unit of thelower limit of the range, unless the context clearly dictates otherwise.

This application refers to various issued patents, published patentapplications, journal articles, and other publications, all of which areincorporated herein by reference. If there is a conflict between any ofthe incorporated references and the instant specification, thespecification shall control. In addition, any particular embodiment ofthe present invention that falls within the prior art may be explicitlyexcluded from any one or more of the claims. Because such embodimentsare deemed to be known to one of ordinary skill in the art, they may beexcluded even if the exclusion is not set forth explicitly herein. Anyparticular embodiment of the invention can be excluded from any claim,for any reason, whether or not related to the existence of prior art.

Those skilled in the art will recognize or be able to ascertain using nomore than routine experimentation many equivalents to the specificembodiments described herein. The scope of the present embodimentsdescribed herein is not intended to be limited to the above Description,but rather is as set forth in the appended claims. Those of ordinaryskill in the art will appreciate that various changes and modificationsto this description may be made without departing from the spirit orscope of the present invention, as defined in the following claims.

What is claimed is:
 1. A compound of Formula (I):

or a pharmaceutically acceptable salt thereof; wherein: Ring A is acarbocyclic, heterocyclic, heteroaryl, or aryl ring; each instance ofR^(A) is independently selected from the group consisting of hydrogen,halogen, optionally substituted acyl, optionally substituted alkyl,optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, optionally substituted heteroaryl,—OR^(A1), —N(R^(A1))2, and —SR^(A1), wherein each occurrence of R^(A1)is independently selected from the group consisting of hydrogen, acyl,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, a nitrogen protecting group when attached to anitrogen atom, an oxygen protecting group when attached to an oxygenatom, a sulfur protecting group when attached to a sulfur atom, or twoR^(A1) groups are joined to form an optionally substituted heterocyclicring; m is 0, 1, 2, 3, or 4; Ring B is a group of the formula:

R^(B1) is selected from the group consisting of hydrogen, halogen,optionally substituted acyl, optionally substituted alkyl, optionallysubstituted alkenyl, optionally substituted alkynyl, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, optionally substituted heteroaryl, —OR^(B1a),—N(R^(B1a))₂, and —SR^(B1a), wherein each occurrence of R^(B1a) isindependently selected from the group consisting of hydrogen, acyl,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, a nitrogen protecting group when attached to anitrogen atom, an oxygen protecting group when attached to an oxygenatom, a sulfur protecting group when attached to a sulfur atom, or twoR^(B1a) groups are joined to form an optionally substituted heterocyclicring; W_(B) is N or CR^(B2), wherein R^(B2) is selected from the groupconsisting of hydrogen, halogen, optionally substituted acyl, optionallysubstituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, —OR^(B2a), —N(R^(B2a))₂, and —SR^(B2a), whereineach occurrence of R^(B2a) is independently selected from the groupconsisting of hydrogen, acyl, optionally substituted alkyl, optionallysubstituted alkenyl, optionally substituted alkynyl, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, optionally substituted heteroaryl, a nitrogenprotecting group when attached to a nitrogen atom, an oxygen protectinggroup when attached to an oxygen atom, a sulfur protecting group whenattached to a sulfur atom, or two R^(B2a) groups are joined to form anoptionally substituted heterocyclic ring; optionally wherein R^(B1) andR^(B2) are joined to form an optionally substituted carbocyclyl,optionally substituted heterocyclyl, optionally substituted heteroaryl,or optionally substituted aryl ring; L₁ is a bond directly attachingRing A to Ring B, or L₁ is ═C(R^(L1a))—, —O—, —S—, —NR^(L1b)—,—NR^(L1b)C(═O)—, —C(═O)NR^(L1b)—, —SC(═O)—, —C(═O)S—, —OC(═O)—,—C(=O)O—, —NR^(L1b)C(═S)—, —C(═S)NR^(L1b)—, trans-CH═CH—, cis-CH═CH—,—S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(L1b)—, —NR^(L1b)S(═O)₂—, or anoptionally substituted C₁₋₄ hydrocarbon chain, optionally wherein onemethylene unit of the hydrocarbon chain is replaced with ═C(R^(L1a))—,—O—, —S—, —NR^(L1b)—, —NR^(L1b)C(═O)—, —C(═O)NR^(L1b)—, —SC(═O)—,—OC(═O)S—, —O(═O)—, —C(═O)O—, —NR^(L1b)C(═S)—, —C(═S)NR^(L1b)—,trans-CH═CH—, cis-CH═CH—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(L1b)—, or—NR^(L1b)S(═O)₂—, wherein R^(L1a) is hydrogen, halogen, optionallysubstituted acyl, optionally substituted alkyl, optionally substitutedalkenyl, optionally substituted alkynyl, optionally substitutedcarbocyclyl, optionally substituted heterocyclyl, optionally substitutedaryl, optionally substituted heteroaryl, —CN, or —NO₂, and R^(L1b) ishydrogen, C₁₋₆ alkyl, or a nitrogen protecting group;

represents a single or double bond; X is an optionally substituted C₁₋₄hydrocarbon chain, optionally wherein one or more carbon units of thehydrocarbon chain is replaced with —O—, —S—, or —NR^(X)—, wherein R^(X)is hydrogen, C₁₋₆ alkyl, or a nitrogen protecting group; L₂ is a bond,—O—, —S—, —NR^(L2a)—, —NR^(L2a)C(═O)—, —C(═O)NR^(L2a)—, —SC(═O)—,—C(═O)S—, —OC(═O)—, —C(═O)O—, —NR^(L2a)C(═S)—, —C(═S)NR^(L2a)—,trans-CR^(L2b)═CR^(L2b)—, cis-CR^(L2b)═CR^(L2b)—, —C≡C—, —OC(R^(L2b))₂—,—C(R^(L2b))₂O—, —NR^(L2a)C(R^(L2b))₂—, —C(R^(L2b))₂NR^(L2a)—,SC(R^(L2b))₂—, —C(R^(L2b))₂S—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(L2a)—,—NR^(L2a)S(═O)₂—, or an optionally substituted C₁₋₄ hydrocarbon chain,optionally wherein one or more carbon units of the hydrocarbon chain isreplaced with —O—, —S—, —NR^(L2a)—, —NR^(L2a)C(═O)—, —C(═O)NR^(L2a)—,—SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NR^(L2a)C(═S)—,—C(═S)NR^(L2a)—, trans-CR^(L2b)═CR^(L2b)—, cis-CR^(L2b)═CR^(L2b)—,—C≡C—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(L2a)—, or —NR^(L2a)S(═O)₂—,wherein R^(L2a) is hydrogen, C₁₋₆ alkyl, or a nitrogen protecting group,and wherein each occurrence of R^(L2b) is independently selected fromthe group consisting of hydrogen, halogen, optionally substituted alkyl,optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, and optionally substituted heteroaryl, ortwo R^(L2b) groups are joined to form an optionally substitutedcarbocyclic or optionally substituted heterocyclic ring; each instanceof R^(C) is independently selected from the group consisting ofhydrogen, halogen, optionally substituted acyl, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, optionally substituted heteroaryl,—OR^(C1), —N(R^(C1))₂, and —SR^(C1), wherein each occurrence of R^(C1)is independently selected from the group consisting of hydrogen, acyl,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, a nitrogen protecting group when attached to anitrogen atom, an oxygen protecting group when attached to an oxygenatom, a sulfur protecting group when attached to a sulfur atom, or twoR^(C1) groups are joined to form an optionally substituted heterocyclicring; n is 0, 1, 2, 3, or 4; each instance of R^(D) is independentlyselected from the group consisting of hydrogen, halogen, optionallysubstituted acyl, optionally substituted alkyl, optionally substitutedalkenyl, optionally substituted alkynyl, optionally substitutedcarbocyclyl, optionally substituted heterocyclyl, optionally substitutedaryl, optionally substituted heteroaryl, —OR^(D1), —N(R^(D1))₂, and—SR^(D1), wherein each occurrence of R^(D1) is independently selectedfrom the group consisting of hydrogen, acyl, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, optionally substituted heteroaryl, anitrogen protecting group when attached to a nitrogen atom, an oxygenprotecting group when attached to an oxygen atom, a sulfur protectinggroup when attached to a sulfur atom, or two R^(D1) groups are joined toform an optionally substituted heterocyclic ring; p is 0, 1, 2, 3, or 4;R^(E) is a group of the formula:

wherein: L₃ is a bond, —O—, —S—, —NR^(L3a), —NR^(L3a)C(═O)—,—C(═O)NR^(L3a)—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—,—NR^(L3a)C(═S)—, —C(═S)NR^(L3a)—, trans-CR^(L3b)═CR^(L3b)—,cis-CR^(L3b)═CR^(L3b)—, —C≡C—, —OC(R^(L3b))₂—, —C(R^(L3b))₂O—,—NR^(L3a)C(R^(L3b))₂—, —C(R^(L3b))₂NR^(L3a)—, —SC(R^(L3b))₂—,—C(R^(L3b))₂S—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(L3a)—,—NR^(L3a)S(═O)₂—, or an optionally substituted C₁₋₄ hydrocarbon chain,optionally wherein one or more carbon units of the hydrocarbon chain isreplaced with —O—, —S—, —NR^(L3a)—, —NR^(L3a)C(═O)—, —C(═O)NR^(L3a)—,—SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NR^(L3a)C(═S)—,—C(═S)NR^(L3a)—, trans-CR^(L3b)═CR^(L3b)—, cis-CR^(L3b)═CR^(L3b)—,—C≡C—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(L3a)—, or —NR^(L3a)S(═O)₂—,wherein R^(L3a) is hydrogen, C₁₋₆ alkyl, or a nitrogen protecting group,and wherein each occurrence of R^(L3b) is independently selected fromthe group consisting of hydrogen, halogen, optionally substituted alkyl,optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, and optionally substituted heteroaryl, ortwo R^(L3b) groups are joined to form an optionally substitutedcarbocyclic or optionally substituted heterocyclic ring; L₄ is a bond oran optionally substituted C₁₋₄ hydrocarbon chain; R^(E1) is selectedfrom the group consisting of hydrogen, halogen, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, optionally substituted heteroaryl,—CH₂OR^(E1a), —CH₂N(R^(E1a))₂, —CH₂SR^(E1a), —OR^(E1a), —N(R^(E1a))₂,and —SR^(E1a), wherein each occurrence of R^(E1a) is independentlyselected from the group consisting of hydrogen, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, and optionally substituted heteroaryl, ortwo R^(E1a) groups are joined to form an optionally substitutedheterocyclic ring; R^(E2) is selected from the group consisting ofhydrogen, halogen, optionally substituted alkyl, optionally substitutedalkenyl, optionally substituted alkynyl, optionally substitutedcarbocyclyl, optionally substituted heterocyclyl, optionally substitutedaryl, optionally substituted heteroaryl, —CH₂OR^(E2a), —CH₂N(R^(E2a))₂,—CH₂SR^(E2a), —OR^(E2a), —N(R^(E2a))₂, and —SR^(E2a), wherein eachoccurrence of R^(E2a) is independently selected from the groupconsisting of hydrogen, optionally substituted alkyl, optionallysubstituted alkenyl, optionally substituted alkynyl, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, and optionally substituted heteroaryl, or two R^(E2a)groups are joined to form an optionally substituted heterocyclic ring;R^(E3) is selected from the group consisting of hydrogen, halogen,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, —CH₂OR^(E3a), —CH₂N(R^(E3a))₂, —CH₂SR^(E3a),—OR^(E3a), —N(R^(E3a))₂, and —SR^(E3a), wherein each occurrence ofR^(E3a) is independently selected from the group consisting of hydrogen,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, and optionallysubstituted heteroaryl, or two R^(E3a) groups are joined to form anoptionally substituted heterocyclic ring; optionally wherein R^(E1) andR^(E3) or R^(E2) and R^(E3) or R^(E1) and R^(E2) are joined to form anoptionally substituted carbocyclic or optionally substitutedheterocyclic ring; R^(E4) is a leaving group; Y is O, S, or NR^(E5),wherein R^(E5) is hydrogen, C₁₋₆ alkyl, or a nitrogen protecting group;a is 1 or 2; and z is 0, 1, 2, 3, 4, 5, or
 6. 2-48. (canceled)
 49. Thecompound of claim 1, wherein the compound is of formula:

or a pharmaceutically acceptable salt thereof.
 50. A pharmaceuticalcomposition comprising a compound of claim 1, or a pharmaceuticallyacceptable salt thereof, and a pharmaceutically acceptable excipient.51. A method of treating a proliferative disease comprisingadministering to a subject in need thereof an effective amount of acompound of claim 1, or a pharmaceutically acceptable salt thereof. 52.A method of treating a neurodegenerative disease comprisingadministering to a subject in need thereof an effective amount of acompound of claim 1, or a pharmaceutically acceptable salt thereof. 53.A method of treating stroke comprising administering to a subject inneed thereof an effective amount of a compound of claim 1, or apharmaceutically acceptable salt thereof.
 54. A method of treatingParkinson's disease comprising administering to a subject in needthereof an effective amount of a compound of claim 1, or apharmaceutically acceptable salt thereof.
 55. A method of treatingAlzheimer's disease comprising administering to a subject in needthereof an effective amount of a compound of claim 1, or apharmaceutically acceptable salt thereof.
 56. A method of treating aninflammatory disease comprising administering to a subject in needthereof an effective amount of a compound of claim 1, or apharmaceutically acceptable salt thereof.
 57. A method of treating ametabolic disorder comprising administering to a subject in need thereofan effective amount of a compound of claim 1, or a pharmaceuticallyacceptable salt thereof.
 58. A method of treating diabetes comprisingadministering to a subject in need thereof an effective amount of acompound of claim 1, or a pharmaceutically acceptable salt thereof.59-68. (canceled)
 69. A method of treating a JNK mediated condition, themethod comprising administering to a subject in need thereof aneffective amount of a compound of claim 1, or a pharmaceuticallyacceptable salt thereof.
 70. A method of treating a CDK7 mediatedcondition, the method comprising administering to a subject in needthereof an effective amount of a compound of claim 1, or apharmaceutically acceptable salt thereof.
 71. A method of treating anIRAK1/4 mediated condition, the method comprising administering to asubject in need thereof an effective amount of a compound of claim 1, ora pharmaceutically acceptable salt thereof.
 72. A method of treating anEGFR mediated condition, the method comprising administering to asubject in need thereof an effective amount of a compound of claim 1, ora pharmaceutically acceptable salt thereof.
 73. A method of treating aDDR1/2 mediated condition, the method comprising administering to asubject in need thereof an effective amount of a compound of claim 1, ora pharmaceutically acceptable salt thereof.
 74. A method of treating ac-Kit mediated condition, the method comprising administering to asubject in need thereof an effective amount of a compound of claim 1, ora pharmaceutically acceptable salt thereof.
 75. A method of treating aPDGFR mediated condition, the method comprising administering to asubject in need thereof an effective amount of a compound of claim 1, ora pharmaceutically acceptable salt thereof.
 76. A method of screening alibrary of compounds of claim 1 to identify one or more compounds thatare useful in the treatment of a proliferative disease in a subject, themethod comprising: providing at least two different compounds of claim1, or pharmaceutically acceptable salts thereof; and performing at leastone assay using the different compounds, or pharmaceutically acceptablesalts thereof, to detect one or more characteristics associated with theproliferative disease. 77-85. (canceled)